User: Mathieu Gendarme

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10 months ago
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Posts by Mathieu Gendarme

<prev • 21 results • page 1 of 3 • next >
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Comment: C: EBimage fftw issue
... Thanks a lot Wolfgang. Indeed I knew that it is not an EBImage issue but more how the fftw library was retrieved. I installed on my local environment fftw3 again using anaconda and specified where the library was supposed to be with LD_LIBRARY_PATH and it worked. Thanks again. Cheers ...
written 7 weeks ago by Mathieu Gendarme20
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EBimage fftw issue
... Dear all, I am trying to run a bash file calling an R script on a cluster running CentOS 7. My R sessionInfo looks like this: > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: defau ...
ebimage centos written 7 weeks ago by Mathieu Gendarme20 • updated 7 weeks ago by Wolfgang Huber13k
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Comment: C: EBImage computeFeatures error
... Dear all, I have made some progress in understanding where the issue is coming from. When I compute individually computeFeatures.basic; computeFeatures.moment; computeFeatures.shape; they return the same amount of rows, however computeFeatures.haralick retrieves a higher amount of rows indicating t ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... Thank you very much Andrzej! You pointed out that the data might not be the right one and you are correct, with the data of my first archive file I do not get an error. Here is the proper data set leading to a failure at position "00005": https://www.dropbox.com/s/uog8u6upvlwblxd/IF015_plate002_p ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... OK that works as well. Please find the two objects here: https://www.dropbox.com/s/v6y8o0z5vqaj3k8/Donut.RData?dl=0 https://www.dropbox.com/s/nu0888x0nwtti18/Img488.RData?dl=0 Cheers ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... The output of ImageProcessing(Image = AllImages, Plate = 2, Well = "A5", Position = "00005") with options(error=recover) doesn't change to much. > ImageProcessing(Image = AllImages, Plate = 2, Well = "A5", Position = "00005") Error in (function (..., deparse.level = 1) : number of rows of ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... Hi Andrzej, I would love to provide the Donut mask and the Img488 outputs. However I have a problem with the Donut, when I want to writeImage it rescales the labels and transforms everything above 0 to 1s. If I do normalize than I get individual values for each mask but not integers which I assume ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... Thanks Andrzej for trying it out, Here is what get from the traceback: [1] "Plate: 2; Well: A5; Position: 00001; Time:2018-11-21 12:32:21" [1] "Plate: 2; Well: A5; Position: 00002; Time:2018-11-21 12:32:41" [1] "Plate: 2; Well: A5; Position: 00003; Time:2018-11-21 12:32:56" [1] "Plate: 2; Well: A ...
written 3 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... Just to mention I did try to run this as well on a linux machine with ubuntu 18.04 and get the exact same message... Very strange that it doesn't happen to you Mike. Something must be wrong at my side. ...
written 4 months ago by Mathieu Gendarme20
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Comment: C: EBImage computeFeatures error
... I also did try your script Mike and I get the exact same issue. I really don't know anymore how to tackle this problem. ...
written 4 months ago by Mathieu Gendarme20

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