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flatironinstitute / mountainlab-js

MountainLab is data processing, sharing and visualization software for scientists. It is built around MountainSort, spike sorting software, but is designed to be more generally applicable.
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Unable to use qt-mountainview #73

Closed yukidai closed 5 years ago

yukidai commented 5 years ago

Hi, I'm trying to visualize my data using qt-mountainview but it seems like that the ml-prv-create function fails to create prv files on my computer. Please take a look at it. Thank you very much!

After tying in:

qt-mountainview --raw=raw.mda.prv --filt=filt.mda --pre=pre.mda --firings=firings_raw.mda --cluster_metrics=metrics_tagged.json --samplerate=30000

It returned:

GLib-GIO-Message: 10:54:41.034: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications. qt-mountainview ; origin: /home/tjd/anaconda3/conda-bld/git_cache/github.com/flatironinstitute/qt-mountainview ; commit: heads/master-0-gff77bac Compiled using Qt version: 5.6.2 (/home/user/conda/envs/mlab on host: 'rime' Setting up object registry... Parsing command-line parameters... Creating MVContext... Setting up context... Creating prv object for: filt.mda Creating prv object for: pre.mda Creating prv object for: firings_raw.mda Setting up main window... Adding controls to main window... Opening initial views... Starting event loop... [ Getting processor spec... ] [ Checking inputs and substituting prvs ... ] [ Computing process signature ... ] /tmp/EE11_01_20180604.nt1.mountain/firings_raw.mda (node:17436) UnhandledPromiseRejectionWarning: TypeError: Cannot read property 'original_checksum' of undefined at /home/user/conda/envs/mlab/lib/node_modules/mountainlab/mlproc/prv_utils.js:203:24 at /home/user/conda/envs/mlab/lib/node_modules/mountainlab/mlproc/prv_utils.js:192:7 (node:17436) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1) (node:17436) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code. ":::: Failed to open DiskReadMda32 file: /tmp/mountainlab-tmp/tmp_long_term/41796105db66a8dced781f086f21cd6db0a8be22_templates_out.tmp" "File does not exist: /tmp/mountainlab-tmp/tmp_long_term/41796105db66a8dced781f086f21cd6db0a8be22_templates_out.tmp" Unable to read chunk of templates in cluster detail view

I also tried to use the ml-prv-create function directly and it returned error messages:

Creating prv record for file ... : pre.mda (node:16338) UnhandledPromiseRejectionWarning: TypeError: console.err is not a function at /home/user/conda/envs/mlab/lib/node_modules/mountainlab/mlproc/prv_utils.js:72:15 at /home/user/conda/envs/mlab/lib/node_modules/mountainlab/mlproc/prv_utils.js:192:7 (node:16338) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1) (node:16338) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.

alexmorley commented 5 years ago

Hi there! Could you please post the output for ml-prv-locate raw.mda.prv? If it finds a file it would be work to check that file exists.

I think there may be a bug here as well but it could be a day or two before someone has a chance to fix.

alexmorley commented 5 years ago

@magland I haven't looked into this yet but it seems prv_create is failing silently and returning undefined instead of an error.

(node:17436) UnhandledPromiseRejectionWarning: TypeError: Cannot read property 'original_checksum' of undefined
at /home/user/conda/envs/mlab/lib/node_modules/mountainlab/mlproc/prv_utils.js:203:24
yukidai commented 5 years ago

I tried with

ml-prv-locate raw.mda.prv

And it returned with the correct location of my data:

/media/user/DATA/Projects/eeyd_a5GABA_Project/EE11_FF+_Experiment/EE11/01_20180604/EE11_01_20180604.mda/EE11_01_20180604.nt1.mda

alexmorley commented 5 years ago

Thanks ... could you also post the exact command you tried with ml-prv-create?

yukidai commented 5 years ago

Yes, its just:

(mlab) user:EE11_01_20180604.nt1.mountain$ ml-prv-create pre.mda

alexmorley commented 5 years ago

Weird! OK thanks I will try and look into this properly this week.

theilmbh commented 5 years ago

Hi all, We had a similar error on a fresh install of mountainlab. We found that the sumit.json and process_cache.json in ~/.mountainlab/database were completely empty on a fresh install, and this seemed to be the cause of the problem. We simply added [] to these empty files and then things would run. I just wanted to bring this to your attention in case anyone else runs in to similar problems.