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juglab / n2v

This is the implementation of Noise2Void training.
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Model does not exist or cannot be loaded #87

Closed XarlesSta closed 4 years ago

XarlesSta commented 4 years ago

I managed to do the training of the data. Nevertheless, every time I tried to do the prediction, I have the same error(see below). Suggestions?

Note: I am trying this on my local PC using Fiji. I have not tried yep using Jupyter notebook. I did the training as well in Fiji.

name=Thu Jun 25 16:43:12 PDT 2020 last checkpoint, description=null, cite=[{text=Krull, A. and Buchholz, T. and Jug, F. Noise2void - learning denoising from single noisy images. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (2019), doi=arXiv:1811.10980}], authors=null, documentation=null, tags=[denoising, unet2d], license=null, format_version=0.2.0-csbdeep, language=java, framework=tensorflow, source=n2v, test_input=testinput.tif, test_output=testoutput.tif, inputs=[{name=input, axes=byxc, data_type=float32, data_range=[-inf, inf], halo=[0, 22, 22, 0], shape={min=[1, 16, 16, 1], step=[1, 16, 16, 0]}}], outputs=[{name=activation_11/Identity, axes=byxc, data_type=float32, data_range=[-inf, inf], shape={reference_input=input, scale=[1.0, 1.0, 1.0, 1.0], offset=[0, 0, 0, 0]}}], training={source=de.csbdresden.n2v.train.N2VTraining, kwargs={batchSize=64, learningRate=4.0E-4, trainDimensions=2, neighborhoodRadius=5, numEpochs=300, numStepsPerEpoch=200, patchShape=64, stepsFinished=60000}}, prediction={weights={source=./variables/variables}, preprocess=[{spec=de.csbdresden.n2v.predict.N2VPrediction::preprocess, kwargs={mean=[193.19666], stdDev=[30.815493]}}], postprocess=[{spec=de.csbdresden.n2v.predict.N2VPrediction::postprocess, kwargs={mean=[193.19666], stdDev=[30.815493]}}], dependencies=./dependencies.yaml}} N2V prediction mean : 193.19666 N2V prediction stdDev: 30.815493 [INFO] Using native TensorFlow version: TF 1.14.0 GPU (CUDA 10.0, CuDNN >= 7.4.1) [INFO] Loading TensorFlow model Thu Jun 25 16:43:12 PDT 2020 last checkpoint 2020-06-25T23:43:12.563207Z from source file file:/C:/Users/GarzonCoral/Desktop/n2v-3850187345415030802.bioimage.io.zip [INFO] Unpacking dependencies.yaml java.io.FileNotFoundException: C:\Fiji.app\models\Thu Jun 25 16:43:12 PDT 2020 last checkpoint 2020-06-25T23:43:12.563207Z\dependencies.yaml (The filename, directory name, or volume label syntax is incorrect) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at net.imagej.tensorflow.util.UnpackUtil.unZip(UnpackUtil.java:149) at net.imagej.tensorflow.util.UnpackUtil.unZip(UnpackUtil.java:131) at net.imagej.tensorflow.DefaultTensorFlowService.downloadAndUnpackResource(DefaultTensorFlowService.java:407) at net.imagej.tensorflow.DefaultTensorFlowService.modelDir(DefaultTensorFlowService.java:384) at net.imagej.tensorflow.DefaultTensorFlowService.loadCachedModel(DefaultTensorFlowService.java:131) at net.imagej.modelzoo.consumer.model.tensorflow.TensorFlowModel.loadModelFile(TensorFlowModel.java:145) at net.imagej.modelzoo.consumer.model.tensorflow.TensorFlowModel.loadModel(TensorFlowModel.java:110) at net.imagej.modelzoo.DefaultModelZooArchive.createModelInstance(DefaultModelZooArchive.java:101) at net.imagej.modelzoo.consumer.DefaultModelZooPrediction.loadModel(DefaultModelZooPrediction.java:107) at net.imagej.modelzoo.consumer.DefaultModelZooPrediction.run(DefaultModelZooPrediction.java:81) at de.csbdresden.n2v.predict.N2VPrediction.run(N2VPrediction.java:89) at de.csbdresden.n2v.predict.N2VPrediction.predictPadded(N2VPrediction.java:105) at de.csbdresden.n2v.command.N2VPredictCommand.run(N2VPredictCommand.java:123) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [ERROR] Model does not exist or cannot be loaded. Exiting.

tibuch commented 4 years ago

Hi @XarlesSta

Thank you for reporting. I will move this issue to N2V in Fiji.