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neurodata / ndstore

code for storing neurodata images and image annotations
http://neurodata.io
Apache License 2.0
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imgUpload throwing "NameError: global name 'datasetSize' is not defined" #375

Closed toekneesunshine closed 8 years ago

toekneesunshine commented 8 years ago

I'm trying to ingest a histogram equalized version of the CLARITY brain Aut1367 into ndstore. Since the Aut1367 data already exists in ndstore, I downloaded the image and then applied our histogram equalization technique. The technique outputs a numpy array, which I then convert into a simpleITK image (following the last steps in the ndreg tutorial, whereby they upload a simpleITK img: https://github.com/neurodata/ndreg/blob/master/doc/3D_CLARITY_RegistrationAndAnalysis.ipynb).

I then created an OpenConnectome account and made a private dataset called "Aut1367_histeq", with token as "Aut1367_tony" and channel as "histogram_equalization". I set the X image size, Y image size, Z image size on my ndstore dataset to the values I got from the image dimensions. However, when I call imgUpload as follows:

token = "Aut1367_tony" channel = "histogram_equalization" imgUpload(Aut1367_histeq_ITK, token, channel)

I get a "NameError: global name 'datasetSize' is not defined".

Am I missing something? Is there a way for me to efficiently upload these histogram equalized ITK snap images with imgUpload?

kunallillaney commented 8 years ago

@toekneesunshine I need more details. Which server are you running this on? Also, have you verified if this an ndio issue or not? I need the RESTful call this is making to debug this not the function you are calling in ndio.

kunallillaney commented 8 years ago

@toekneesunshine Any updates? @jovo

toekneesunshine commented 8 years ago

@kunallillaney The raw data is on a GoogleCloud instance. After looking through the error message, it seems to more likely be a problem with one of the ndreg functions (specifically, this imgUpload function) -- I'll make an issue there instead.

kunallillaney commented 8 years ago

Okay. Closing the issue then. @jovo