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fiji_log_out.txt
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fiji_log_out.txt
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STARTED TESTING THE 31 MODELS WITH DEEPIMAGEJ IN FIJI AT 2023-08-03 09:50:45.563625
Logs are in D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\..\test_summaries\fiji_log_out.txt and fiji_log_err.txt
* MODEL 1/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406803/6406804/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: shivering-raccoon, at 2023-08-03 09:50:57.287000
*** Name: MitchondriaEMSegmentation2D
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
09:51:01 -- Engine: tensorflow-2.7.0-0.4.0-windows-x86_64-cpu-gpu
tensorflow-core-api-0.4.0.jar: [##############################] 100%
total: [##############################] 100%
protobuf-java-3.22.0.jar: [##############################] 100%
total: [##############################] 100%
ndarray-0.3.3.jar: [##############################] 100%
total: [##############################] 100%
tensorflow-core-api-0.4.0-windows-x86_64-gpu.jar: [##############################] 100%
total: [##############################] 100%
javacpp-1.5.8.jar: [##############################] 100%
total: [##############################] 100%
javacpp-1.5.6-windows-x86_64.jar: [##############################] 100%
total: [##############################] 100%
dl-modelrunner-tensorflow-2b-0.3.0.jar: [##############################] 100%
total: [##############################] 100%
09:51:05 -- Engine: tensorflow-1.15.0-1.15.0-windows-x86_64-cpu-gpu
libtensorflow-1.15.0.jar: [##############################] 100%
total: [##############################] 100%
libtensorflow_jni_gpu-1.15.0.jar: [##############################] 100%
total: [##############################] 100%
protobuf-java-3.5.1.jar: [##############################] 100%
total: [##############################] 100%
proto-1.15.0.jar: [##############################] 100%
total: [##############################] 100%
dl-modelrunner-tensorflow-1-0.3.0.jar: [##############################] 100%
total: [##############################] 100%
09:51:08 -- Engine: onnx-17-1.12.1-windows-x86_64-cpu-gpu
onnxruntime_gpu-1.12.1.jar: [##############################] 100%
total: [##############################] 100%
dl-modelrunner-onnx-0.3.1.jar: [##############################] 100%
total: [##############################] 100%
09:51:11 -- Engine: pytorch-1.13.1-1.13.1-windows-x86_64-cpu-gpu
09:51:11 -- Engine: pytorch-2.0.0-2.0.0-windows-x86_64-cpu-gpu
pytorch-jni-2.0.0-0.22.1.jar: [##############################] 100%
total: [####################..........] 67%
pytorch-engine-0.22.1.jar: [##############################] 100%
total: [####################..........] 67%
api-0.22.1.jar: [##############################] 100%
total: [####################..........] 67%
dl-modelrunner-pytorch-0.3.0.jar: [##############################] 100%
total: [##############################] 100%
jna-5.13.0.jar: [##############################] 100%
total: [##############################] 100%
commons-compress-1.22.jar: [##############################] 100%
total: [##############################] 100%
slf4j-api-2.0.6.jar: [##############################] 100%
total: [##############################] 100%
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:128.3344
Standard deviation value:54.6462
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/4
[DEBUG] (Inference) Patch 2/4
[DEBUG] (Inference) Patch 3/4
[DEBUG] (Inference) Patch 4/4
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- MitchondriaEMSegmentation2D_output0_sample_input_0
[DEBUG] Execution of model 'MitchondriaEMSegmentation2D' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406803/6406804/CI_OUTPUT.tif
*** Finished testing model: shivering-raccoon
*** Time taken: 0.7 min, (39 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406803/6406804/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: shivering-raccoon, at 2023-08-03 09:51:48.540000
*** centers of [512, 512, 2, 1, 1] are:
[[128, 257], [128, 257], [0, 2], [0, 1], [0, 1]]
*** Max value: 0.999997735023
*** MSE (relative): 8.2216e-05
*** MSE center (relative): 4.0359e-05
*** MAE (relative): 0.0012748
*** MAE center (relative): 0.0018003
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406803/6406804/output_metrics.json
*** Time taken: 0.0 min, (2 s)
* MODEL 2/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5869899/6647688/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: hiding-tiger, at 2023-08-03 09:52:02.611000
*** Name: LiveCellSegmentationBoundaryModel
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:128.0212
Standard deviation value:9.4274
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/4
[DEBUG] (Inference) Patch 2/4
[DEBUG] (Inference) Patch 3/4
[DEBUG] (Inference) Patch 4/4
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- LiveCellSegmentationBoundaryModel_output0_sample_input_0
[DEBUG] Execution of model 'LiveCellSegmentationBoundaryModel' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5869899/6647688/CI_OUTPUT.tif
*** Finished testing model: hiding-tiger
*** Time taken: 0.3 min, (18 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5869899/6647688/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: hiding-tiger, at 2023-08-03 09:52:32.162000
*** centers of [512, 512, 2, 1, 1] are:
[[128, 257], [128, 257], [0, 2], [0, 1], [0, 1]]
*** Max value: 1.0
*** MSE (relative): 0.00015603
*** MSE center (relative): 0.00010112
*** MAE (relative): 0.0037617
*** MAE center (relative): 0.0034222
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5869899/6647688/output_metrics.json
*** Time taken: 0.0 min, (2 s)
* MODEL 3/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7772662/7781091/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: noisy-fish, at 2023-08-03 09:52:45.501000
*** Name: 3D UNet Arabidopsis Ovules Nuclei
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
Pytorch model at:
C:\Users\RUNNER~1\BLANK_~1\Fiji.app\models\the_model\torchscript_tracing.pt
does not coincide with the one specified in the rdf.yaml (incorrect sha256).
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
java.lang.NullPointerException
at DeepImageJ_Run.arrangeParametersAndRunModel(DeepImageJ_Run.java:530)
at DeepImageJ_Run.run(DeepImageJ_Run.java:300)
at ij.IJ.runUserPlugIn(IJ.java:237)
at ij.IJ.runPlugIn(IJ.java:203)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at ij.IJ.run(IJ.java:319)
at ij.IJ.run(IJ.java:409)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:208)
at org.python.core.PyObject.__call__(PyObject.java:494)
at org.python.core.PyObject.__call__(PyObject.java:498)
at org.python.pycode._pyx0.test_one_with_deepimagej$4(D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/fiji_scripts/test_1_with_deepimagej.py:77)
at org.python.pycode._pyx0.call_function(D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/fiji_scripts/test_1_with_deepimagej.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyBaseCode.call(PyBaseCode.java:306)
at org.python.core.PyBaseCode.call(PyBaseCode.java:126)
at org.python.core.PyFunction.__call__(PyFunction.java:416)
at org.python.pycode._pyx0.f$0(D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/fiji_scripts/test_1_with_deepimagej.py:86)
at org.python.pycode._pyx0.call_function(D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/fiji_scripts/test_1_with_deepimagej.py)
at org.python.core.PyTableCode.call(PyTableCode.java:173)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1687)
at org.python.core.__builtin__.eval(__builtin__.java:497)
at org.python.core.__builtin__.eval(__builtin__.java:501)
at org.python.util.PythonInterpreter.eval(PythonInterpreter.java:255)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:57)
at org.python.jsr223.PyScriptEngine.eval(PyScriptEngine.java:31)
at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
at org.scijava.script.ScriptModule.run(ScriptModule.java:164)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7772662/7781091/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: noisy-fish, at 2023-08-03 09:52:56.836000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7772662/7781091/output_metrics.json
* MODEL 4/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5847355/6647683/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: powerful-chipmunk, at 2023-08-03 09:53:07.296000
*** Name: CovidIFCellSegmentationBoundaryModel
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:1752.8062
Standard deviation value:487.4528
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/4
[DEBUG] (Inference) Patch 2/4
[DEBUG] (Inference) Patch 3/4
[DEBUG] (Inference) Patch 4/4
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- CovidIFCellSegmentationBoundaryModel_output0_sample_input_0
[DEBUG] Execution of model 'CovidIFCellSegmentationBoundaryModel' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5847355/6647683/CI_OUTPUT.tif
*** Finished testing model: powerful-chipmunk
*** Time taken: 0.3 min, (18 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5847355/6647683/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: powerful-chipmunk, at 2023-08-03 09:53:36.079000
*** centers of [512, 512, 2, 1, 1] are:
[[128, 257], [128, 257], [0, 2], [0, 1], [0, 1]]
*** Max value: 0.999992489815
*** MSE (relative): 0.00049216
*** MSE center (relative): 0.0001432
*** MAE (relative): 0.0040984
*** MAE center (relative): 0.0028319
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5847355/6647683/output_metrics.json
*** Time taken: 0.0 min, (2 s)
* MODEL 5/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334383/7805067/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: pioneering-rhino, at 2023-08-03 09:53:49.535000
*** Name: 2D UNet Arabidopsis Ovules
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/1
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
[DEBUG] Execution of model '2D UNet Arabidopsis Ovules' completed.
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334383/7805067/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: pioneering-rhino, at 2023-08-03 09:54:05.498000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334383/7805067/output_metrics.json
* MODEL 6/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874741/5874742/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: impartial-shrimp, at 2023-08-03 09:54:15.957000
*** Name: Neuron Segmentation in EM (Membrane Prediction)
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:126.0766
Standard deviation value:32.7007
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/8
[DEBUG] (Inference) Patch 2/8
[DEBUG] (Inference) Patch 3/8
[DEBUG] (Inference) Patch 4/8
[DEBUG] (Inference) Patch 5/8
[DEBUG] (Inference) Patch 6/8
[DEBUG] (Inference) Patch 7/8
[DEBUG] (Inference) Patch 8/8
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- Neuron Segmentation in EM (Membrane Prediction)_output0_sample_input_0
[DEBUG] Execution of model 'Neuron Segmentation in EM (Membrane Prediction)' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874741/5874742/CI_OUTPUT.tif
*** Finished testing model: impartial-shrimp
*** Time taken: 2.6 min, (156 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874741/5874742/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: impartial-shrimp, at 2023-08-03 09:57:03.924000
*** centers of [360, 360, 1, 32, 1] are:
[[90, 181], [90, 181], [0, 1], [8, 17], [0, 1]]
*** Max value: 1.0
*** MSE (relative): 0.014321
*** MSE center (relative): 0.0001323
*** MAE (relative): 0.024155
*** MAE center (relative): 0.0031592
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874741/5874742/output_metrics.json
*** Time taken: 0.2 min, (13 s)
* MODEL 7/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7274275/8123818/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: joyful-deer, at 2023-08-03 09:57:28.241000
*** Name: CebraNET Cellular Membranes in Volume SEM
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Error loading Pytorch model: CebraNET Cellular Membranes in Volume SEM
Check that the Pytorch version corresponds to the pytorch-native-auto jar executable.
If the problem persits, please check the DeepImageJ Wiki.
Load model error: false
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7274275/8123818/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: joyful-deer, at 2023-08-03 09:57:40.016000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7274275/8123818/output_metrics.json
* MODEL 8/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/fiji/N2VSEMDemo/latest/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: None, at 2023-08-03 09:57:50.321000
*** Name: N2V SEM Demo
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/4
Error applying the model
Note that in Pytorch <=1.6.0 the batch dimension should not be provided, it is added automatically.
[DEBUG] Close all the inputs except the input image
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/fiji/N2VSEMDemo/latest/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: None, at 2023-08-03 09:58:15.048000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/fiji/N2VSEMDemo/latest/output_metrics.json
* MODEL 9/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334881/7805026/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: laid-back-lobster, at 2023-08-03 09:58:25.162000
*** Name: 2D UNet Arabidopsis Apical Stem Cells
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/1
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
[DEBUG] Execution of model '2D UNet Arabidopsis Apical Stem Cells' completed.
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334881/7805026/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: laid-back-lobster, at 2023-08-03 09:58:38.418000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6334881/7805026/output_metrics.json
* MODEL 10/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6338614/6338615/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: chatty-frog, at 2023-08-03 09:58:48.780000
*** Name: StarDist H&E Nuclei Segmentation
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Percentile normalization to the axes: xy
with min_percentile: 0.01
and max_percentile: 0.998
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/6
[DEBUG] (Inference) Patch 2/6
[DEBUG] (Inference) Patch 3/6
[DEBUG] (Inference) Patch 4/6
[DEBUG] (Inference) Patch 5/6
[DEBUG] (Inference) Patch 6/6
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- StarDist H&E Nuclei Segmentation_output_sample_input_0
[DEBUG] Execution of model 'StarDist H&E Nuclei Segmentation' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6338614/6338615/CI_OUTPUT.tif
*** Finished testing model: chatty-frog
*** Time taken: 0.3 min, (20 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6338614/6338615/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: chatty-frog, at 2023-08-03 09:59:19.537000
*** centers of [512, 304, 33, 1, 1] are:
[[128, 257], [76, 153], [8, 17], [0, 1], [0, 1]]
*** Max value: 35.1791687012
*** MSE (relative): 0.02642
*** MSE center (relative): 0.0041312
*** MAE (relative): 0.010532
*** MAE center (relative): 0.0071758
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6338614/6338615/output_metrics.json
*** Time taken: 0.3 min, (16 s)
* MODEL 11/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7380171/7405349/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: easy-going-sauropod, at 2023-08-03 09:59:46.663000
*** Name: Drosophila epithelia cell boundary segmentation of 2D projections
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/1
Error applying the model
Note that in Pytorch <=1.6.0 the batch dimension should not be provided, it is added automatically.
[DEBUG] Close all the inputs except the input image
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7380171/7405349/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: easy-going-sauropod, at 2023-08-03 10:00:22.049000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.7380171/7405349/output_metrics.json
* MODEL 12/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6383429/7774505/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: loyal-squid, at 2023-08-03 10:00:32.100000
*** Name: 3D UNet Mouse Embryo Fixed
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/8
[DEBUG] (Inference) Patch 2/8
[DEBUG] (Inference) Patch 3/8
[DEBUG] (Inference) Patch 4/8
[DEBUG] (Inference) Patch 5/8
[DEBUG] (Inference) Patch 6/8
[DEBUG] (Inference) Patch 7/8
[DEBUG] (Inference) Patch 8/8
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
[DEBUG] Execution of model '3D UNet Mouse Embryo Fixed' completed.
Exited engine ClassLoader
[DEBUG] End execution
There are no images open
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6383429/7774505/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: loyal-squid, at 2023-08-03 10:00:54.946000
*** Run did not produce output
*** Empty metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6383429/7774505/output_metrics.json
* MODEL 13/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6811491/6811492/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: independent-shrimp, at 2023-08-03 10:01:05.198000
*** Name: EnhancerMitochondriaEM3D
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Percentile normalization to the axes: xyz
with min_percentile: 0.01
and max_percentile: 1
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/8
[DEBUG] (Inference) Patch 2/8
[DEBUG] (Inference) Patch 3/8
[DEBUG] (Inference) Patch 4/8
[DEBUG] (Inference) Patch 5/8
[DEBUG] (Inference) Patch 6/8
[DEBUG] (Inference) Patch 7/8
[DEBUG] (Inference) Patch 8/8
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- EnhancerMitochondriaEM3D_output0_sample_input_0
[DEBUG] Execution of model 'EnhancerMitochondriaEM3D' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6811491/6811492/CI_OUTPUT.tif
*** Finished testing model: independent-shrimp
*** Time taken: 1.8 min, (108 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6811491/6811492/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: independent-shrimp, at 2023-08-03 10:03:05.069000
*** centers of [256, 256, 2, 32, 1] are:
[[64, 129], [64, 129], [0, 2], [8, 17], [0, 1]]
*** Max value: 0.966301560402
*** MSE (relative): 0.028595
*** MSE center (relative): 0.0067275
*** MAE (relative): 0.059246
*** MAE center (relative): 0.04122
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6811491/6811492/output_metrics.json
*** Time taken: 0.2 min, (13 s)
* MODEL 14/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406756/6811922/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: hiding-blowfish, at 2023-08-03 10:03:29.291000
*** Name: EnhancerMitochondriaEM2D
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Percentile normalization to the axes: xy
with min_percentile: 0.01
and max_percentile: 1
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/4
[DEBUG] (Inference) Patch 2/4
[DEBUG] (Inference) Patch 3/4
[DEBUG] (Inference) Patch 4/4
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- EnhancerMitochondriaEM2D_output0_sample_input_0
[DEBUG] Execution of model 'EnhancerMitochondriaEM2D' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406756/6811922/CI_OUTPUT.tif
*** Finished testing model: hiding-blowfish
*** Time taken: 0.3 min, (17 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406756/6811922/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: hiding-blowfish, at 2023-08-03 10:03:57.898000
*** centers of [512, 512, 2, 1, 1] are:
[[128, 257], [128, 257], [0, 2], [0, 1], [0, 1]]
*** Max value: 0.999995589256
*** MSE (relative): 0.0017769
*** MSE center (relative): 0.00052864
*** MAE (relative): 0.0080842
*** MAE center (relative): 0.010371
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6406756/6811922/output_metrics.json
*** Time taken: 0.0 min, (2 s)
* MODEL 15/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6200635/7702687/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: loyal-parrot, at 2023-08-03 10:04:10.995000
*** Name: HPA Cell Segmentation (DPNUnet)
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/1
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- HPA Cell Segmentation (DPNUnet)_output0_sample_input_0
[DEBUG] Execution of model 'HPA Cell Segmentation (DPNUnet)' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6200635/7702687/CI_OUTPUT.tif
*** Finished testing model: loyal-parrot
*** Time taken: 0.3 min, (18 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6200635/7702687/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: loyal-parrot, at 2023-08-03 10:04:40.806000
*** centers of [512, 512, 3, 1, 1] are:
[[128, 257], [128, 257], [0, 3], [0, 1], [0, 1]]
*** Max value: 0.999531149864
*** MSE (relative): 1.9967e-10
*** MSE center (relative): 2.548e-10
*** MAE (relative): 5.6459e-06
*** MAE center (relative): 7.0655e-06
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6200635/7702687/output_metrics.json
*** Time taken: 0.0 min, (3 s)
* MODEL 16/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6028097/6028098/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: organized-badger, at 2023-08-03 10:04:54.844000
*** Name: PlatynereisEMnucleiSegmentationBoundaryModel
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:158.0579
Standard deviation value:31.3358
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/8
[DEBUG] (Inference) Patch 2/8
[DEBUG] (Inference) Patch 3/8
[DEBUG] (Inference) Patch 4/8
[DEBUG] (Inference) Patch 5/8
[DEBUG] (Inference) Patch 6/8
[DEBUG] (Inference) Patch 7/8
[DEBUG] (Inference) Patch 8/8
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- PlatynereisEMnucleiSegmentationBoundaryModel_output0_sample_input_0
[DEBUG] Execution of model 'PlatynereisEMnucleiSegmentationBoundaryModel' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6028097/6028098/CI_OUTPUT.tif
*** Finished testing model: organized-badger
*** Time taken: 1.9 min, (115 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6028097/6028098/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: organized-badger, at 2023-08-03 10:07:01.033000
*** centers of [256, 256, 2, 32, 1] are:
[[64, 129], [64, 129], [0, 2], [8, 17], [0, 1]]
*** Max value: 1.0
*** MSE (relative): 0.038296
*** MSE center (relative): 0.0022729
*** MAE (relative): 0.080934
*** MAE center (relative): 0.012925
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6028097/6028098/output_metrics.json
*** Time taken: 0.2 min, (13 s)
* MODEL 17/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874841/6630266/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: kind-seashell, at 2023-08-03 10:07:25.332000
*** Name: MitochondriaEMSegmentationBoundaryModel
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
Loading: 100% |========================================|
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Mean value:136.8695
Standard deviation value:47.8963
[DEBUG] End pre-processing
[DEBUG] Running inference on the tensors
[DEBUG] (Inference) Patch 1/8
[DEBUG] (Inference) Patch 2/8
[DEBUG] (Inference) Patch 3/8
[DEBUG] (Inference) Patch 4/8
[DEBUG] (Inference) Patch 5/8
[DEBUG] (Inference) Patch 6/8
[DEBUG] (Inference) Patch 7/8
[DEBUG] (Inference) Patch 8/8
[DEBUG] Start post-processing
[DEBUG] End post-processing
[DEBUG] Close all the inputs except the input image
[DEBUG] Open images at the end of the execution:
- MitochondriaEMSegmentationBoundaryModel_output0_sample_input_0
[DEBUG] Execution of model 'MitochondriaEMSegmentationBoundaryModel' completed.
Exited engine ClassLoader
[DEBUG] End execution
*** CI output image saved in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874841/6630266/CI_OUTPUT.tif
*** Finished testing model: kind-seashell
*** Time taken: 5.3 min, (317 s)
** script 2/2: COMPARING TO EXPECTED OUTPUT
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874841/6630266/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started calculating metrics for model: kind-seashell, at 2023-08-03 10:12:54.649000
*** centers of [256, 256, 2, 32, 1] are:
[[64, 129], [64, 129], [0, 2], [8, 17], [0, 1]]
*** Max value: 1.0
*** MSE (relative): 0.0009728
*** MSE center (relative): 3.4836e-05
*** MAE (relative): 0.0046963
*** MAE center (relative): 0.00052943
*** Metrics file written in: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.5874841/6630266/output_metrics.json
*** Time taken: 0.2 min, (13 s)
* MODEL 18/ 31
** script 1/2: TESTING WITH DEEPIMAGEJ HEADLESS
*** The folder is: D:/a/CI-deepimagej-bioimage-io/CI-deepimagej-bioimage-io/python_CI_scripts/../models/10.5281/zenodo.6559474/6559475/
*** wd: D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts
*** Started testing model: naked-microbe, at 2023-08-03 10:13:18.476000
*** Name: Small Extracellular Vesicle TEM Segmentation (Fully Residual U-Net)
engines jars directory is D:\a\CI-deepimagej-bioimage-io\CI-deepimagej-bioimage-io\python_CI_scripts\engines
[DEBUG] Processing image: sample_input_0.tif
[DEBUG] Start loading models
[DEBUG] Finished loading models
[DEBUG] Checking and installing missing engines
[DEBUG] Available Deep Learning frameworks:
-onnx-17 (GPU: true) [CUDA 11.4]
-pytorch-1.13.1 (GPU: true)
-pytorch-2.0.0 (GPU: true)
-tensorflow-1.15.0 (GPU: true) [CUDA 10.0]
-tensorflow-2.7.0 (GPU: true) [CUDA 11.2]
[DEBUG] Engines found
[DEBUG] Loading model
[DEBUG] Image name: sample_input_0.tif
[DEBUG] Start pre-processing
[DEBUG] Run Macro pre-processing
Preprocessing
Error during Java preprocessing.
[DEBUG] Error during Java preprocessing.
Error during the aplication of the model.
Exited engine ClassLoader