Test Report Ci Windows-Latest 3.11 ================================== Environnement ------------- .. list-table:: * - Python - 3.11.9 * - Platform - Windows-10-10.0.26100-SP0 * - CI - true * - System - Windows * - CPU - Intel(R) Xeon(R) Platinum 8370C CPU @ 2.80GHz (2.79 GHz - 2 Cores (4 Logical)) * - RAM - 15.99 GB * - GPU - Error detecting GPU: NVML Shared Library Not Found Summary ------- 240 tests collected, 240 passed ✅, 0 failed ❌, 0 skipped ⏭️ in 0:01:31s on 03/04/2026 at 07:46:07 Monitoring ---------- .. raw:: html
[03-04-2026 07:44:50] Log opened : D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer/log-20260403_074450.log
[03-04-2026 07:44:50] Start Processing.
[03-04-2026 07:44:50] Output folder: D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer
[03-04-2026 07:44:50] Settings saved.
[03-04-2026 07:44:50] Meta file saved.
[03-04-2026 07:44:50] Localization disabled.
[03-04-2026 07:44:50] Loading a pre-computed localization file.
[03-04-2026 07:44:50] File 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer\localizations-20260403_074450.csv' loaded successfully, 451 localization(s) found.
[03-04-2026 07:44:50] Beads Extraction disabled.
[03-04-2026 07:44:50] No pre-computed beads extraction data.
[03-04-2026 07:44:50] Tracking disabled.
[03-04-2026 07:44:50] No pre-computed tracking data.
[03-04-2026 07:44:50] Blinking Reconnection disabled.
[03-04-2026 07:44:50] Tracks Computes disabled.
[03-04-2026 07:44:50] No pre-computed tracks computes data.
[03-04-2026 07:44:50] No pre-computed tracks computes data.
[03-04-2026 07:44:50] No pre-computed tracks computes data.
[03-04-2026 07:44:50] High-resolution visualization disabled.
[03-04-2026 07:44:50] Graphical visualization disabled.
[03-04-2026 07:44:50] Gallery generation disabled.
[03-04-2026 07:44:50] Processing complete.
[03-04-2026 07:44:50] Log closed : D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer/log-20260403_074450.log
Not all valid columns in localizations. Unable to remove ambiguous localizations reliably.
All planes contain multiple localizations. Unable to remove ambiguous localizations reliably.
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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%)
Comparaison avec : 'D:\a\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%)
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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%)
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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%)
Comparaison avec : 'D:\a\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%)
Comparaison avec : 'D:\a\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%)
Comparaison terminée : 269 Points comparés, 269 Points identiques (100.00%)
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\stack-localizations-103.6_True_5_1.0_0.0_7.csv' indisponible.
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\stack-localizations-103.6_False_5_1.0_0.0_7.csv' indisponible.
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\tracking-blinking-2.csv'
Comparaison terminée : 18 Points comparés, 18 Points identiques (100.00%)
Comparaison avec : 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\tracking2-MSD-True.csv'
Comparaison avec : 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\tracking2-Fit-True.csv'
Problem with trajectory identifiers, be careful with filtering
Comparaison avec : 'D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref\tracking2-MSD-False.csv'
Comparaison avec : 'D:\a\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 : 'D:\a\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 : 'D:\a\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 : 'D:\a\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
- Activate : True
- Files : -1
- Mode : 0
{'Files': -1, 'Mode': 0}
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
- Activate : True
- Pixel Size : 0.32
- Exposure : 0.05
- Intensity : 0.012
{'Pixel Size': 0.32, 'Exposure': 0.05, 'Intensity': 0.012}
- 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
- 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, 'Spline Fit Sensor': 0, 'Spline Fit Variance Map': '', 'Spline Fit File': ''}
- Activate : True
- Mode : 2
- Sigma : 1.0
- Theta : 0.0
{'Mode': 2, 'Sigma': 1.0, 'Theta': 0.0}
- Activate : True
- Sensor : 1
- Variance Map :
- File :
{'Sensor': 1, 'Variance Map': '', 'File': ''}
- Activate : True
- Max Distance : 2.0
- 3D : False
{'Max Distance': 2.0, '3D': False}
- Activate : True
- Max Distance : 2.0
{'Max Distance': 2.0}
- Activate : True
- Mode : 1
- Max Duration : 1
- Max Distance : 1.0
{'Mode': 1, 'Max Duration': 1, 'Max Distance': 1.0}
- 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}
- Activate : True
- ROI Size : 11
- ROIs Per Line : 30
{'ROI Size': 11, 'ROIs Per Line': 30}
- Activate : True
- Ratio : 1
- Type : 0
- Source L : 1
- Source T : 1
{'Ratio': 1, 'Type': 0, 'Source L': 1, 'Source T': 1}
- Activate : True
- Mode : 1
- Source : 0
{'Mode': 1, 'Source': 0}
FilteringL id: 1813625063504
X id: 1813729163408
limits id 1813757650816
- Activate : True
- Save : True
- Plane : [1, 100000]
- Localization :
- Activate : True
- X : [0, 100000]
- Y : [0, 100000]
- Z : [-1000, 1000]
- Intensity : [0, 10000000]
- Sigma X : [0.0, 10.0]
- Sigma Y : [0.0, 10.0]
- Circularity : [0.0, 1.0]
- Theta : [-180.0, 180.0]
- 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': [-1000, 1000], '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': [-180.0, 180.0], '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]}
FilteringL id: 1813624738832
X id: 1813786569232
limits id 1813729372416
- Activate : True
- X : [2, 9]
- Y : [0, 100000]
- Z : [-1000, 1000]
- Intensity : [0, 10000000]
- Sigma X : [0.0, 10.0]
- Sigma Y : [0.0, 10.0]
- Circularity : [0.0, 1.0]
- Theta : [-180.0, 180.0]
- MSE XY : [0.0, 1.0]
- MSE Z : [0.0, 1.0]
{'X': [2, 9], 'Y': [0, 100000], 'Z': [-1000, 1000], 'Intensity': [0, 10000000], 'Sigma X': [0.0, 10.0], 'Sigma Y': [0.0, 10.0], 'Circularity': [0.0, 1.0], 'Theta': [-180.0, 180.0], 'MSE XY': [0.0, 1.0], 'MSE Z': [0.0, 1.0]}
- 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]}
Timestamp with hour : 20260403_074511
Timestamp without hour : 20260403
D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\File-03.txt
D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\File-03.txt
Unable to load the DLL 'PALMTracer_File.dll':
Could not find module 'D:\a\palm-tracer\palm-tracer\palm_tracer\DLL\PALMTracer_File.dll' (or one of its dependencies). Try using the full path with constructor syntax.
.
6 entrées.
Timestamps : [0.0, 0.2, 0.41, 0.61, 0.81, 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 : [546.1953125, 546.1953125, 546.1953125, 546.1953125, 546.1953125, 546.171875]
Disk Usage : [0, 0.0, 0.0, 0.0, 0.0, 0.0]
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.
Message d'erreur
Message d'avertissement
Message de succes
D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\ref
D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\output
D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\output
No figures to export.
No valid settings file to load.
INFO: Image file saved successfully.
INFO: Loaded D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack.tif into Napari viewer.
INFO: Loaded D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack.tif into Napari viewer.
INFO: Loaded D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack.tif into Napari viewer.
INFO: Thread Process done.
[03-04-2026 07:46:01] Log opened : D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer/log-20260403_074601.log
[03-04-2026 07:46:01] Start Processing.
[03-04-2026 07:46:01] Output folder: D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer
[03-04-2026 07:46:01] Settings saved.
[03-04-2026 07:46:01] Meta file saved.
[03-04-2026 07:46:01] Localization disabled.
[03-04-2026 07:46:01] No pre-computed localization data.
[03-04-2026 07:46:01] Beads Extraction disabled.
[03-04-2026 07:46:01] No pre-computed beads extraction data.
[03-04-2026 07:46:01] Tracking disabled.
[03-04-2026 07:46:01] No pre-computed tracking data.
[03-04-2026 07:46:01] Blinking Reconnection disabled.
[03-04-2026 07:46:01] Tracks Computes disabled.
[03-04-2026 07:46:01] No pre-computed tracks computes data.
[03-04-2026 07:46:01] No pre-computed tracks computes data.
[03-04-2026 07:46:01] No pre-computed tracks computes data.
[03-04-2026 07:46:01] High-resolution visualization disabled.
[03-04-2026 07:46:01] Graphical visualization disabled.
[03-04-2026 07:46:01] Gallery generation disabled.
[03-04-2026 07:46:01] Processing complete.
[03-04-2026 07:46:01] Log closed : D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack_PALM_Tracer/log-20260403_074601.log
INFO: Thread Process done.
Auto Threshold: 63.95
INFO: Thread Process done.
INFO: Loading the setting file 'C:\Users\runneradmin\.palm_tracer\settings.json'.
INFO: Loaded D:\a\palm-tracer\palm-tracer\palm_tracer\_tests\input\stack.tif into Napari viewer.
WARNING: The file must contain the columns X, Y, Z, and Integrated Intensity.