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unable to view spikes in qt-mountainview, ?sumit, mv #83

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ucnsgy opened this issue Oct 22, 2019 · 0 comments
Open

unable to view spikes in qt-mountainview, ?sumit, mv #83

ucnsgy opened this issue Oct 22, 2019 · 0 comments

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@ucnsgy
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ucnsgy commented Oct 22, 2019

Hi, I am having trouble seeing anything but auto-correlograms with qt-mountainview.
running qt-mountainview after synthesize_dataset.sh ms4_sort_bash.sh returns the error pasted at the bottom.

it looks like mv.mp mv.mv_compute_templates cannot retrieve from or save data to a temporary directory, which is not consistently called. additionally, qt-mountainview creates an odd directory tree in 001_ms4_bash_example folder beginning with " and matching my temporary directory name.

001_ms4_bash_example
├── "
│ └── home
│ └── uskhan
│ └── anaconda3
│ └── envs
│ └── mountainlab
│ └── tmp"
│ ├── ms.-188107830.140478054631296.476707713.tmp.mv2
│ └── sumit
│ └── sha1
│ ├── 96da
│ │ └── 96da05e5447a3ca40db2a027a84d96fc540cf69f
│ ├── c1fc
│ │ └── c1fc30dbcafa36e4fbada2f027498ed820d11759
│ ├── e7e1
│ │ └── e7e18692cefa43f29a7884214ac0308fdefa98dd
│ └── ffe1
│ └── ffe170c37783ef2661830cecd9d7d66f5dc9c3af

===========================
from 001_ms4_bash_example
qt-mountainview --raw dataset/raw.mda.prv --filt output/filt.mda.prv --pre output/pre.mda.prv --samplerate 30000 --firings output/firings.mda

** qt-mountainview ; origin: ; commit:
** Compiled using Qt version: 5.9.7 (/home/uskhan/anaconda3/envs/mountainlab on host: 'liszt2'
Setting up object registry...
Parsing command-line parameters...
Creating MVContext...
Setting up context...
Creating prv object for: output/firings.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 ... ]
Process signature: 7019555dc662700e326add6a37c473ebf0cdb977
[ Checking outputs... ]
{"stdevs_out":""/home/uskhan/anaconda3/envs/mountainlab/tmp"/c3a85fa40a8cb8ca09295f3676bdadc48ea7cdb0_stdevs_out.tmp","templates_out":""/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp"}
Processing ouput - "/home/uskhan/anaconda3/envs/mountainlab/tmp"/c3a85fa40a8cb8ca09295f3676bdadc48ea7cdb0_stdevs_out.tmp
false
{"stdevs_out":"/home/uskhan/anaconda3/envs/mountainlab/mountainsort_examples/bash_examples/001_ms4_bash_example/"/home/uskhan/anaconda3/envs/mountainlab/tmp"/c3a85fa40a8cb8ca09295f3676bdadc48ea7cdb0_stdevs_out.tmp","templates_out":""/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp"}
Processing ouput - "/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp
false
{"stdevs_out":"/home/uskhan/anaconda3/envs/mountainlab/mountainsort_examples/bash_examples/001_ms4_bash_example/"/home/uskhan/anaconda3/envs/mountainlab/tmp"/c3a85fa40a8cb8ca09295f3676bdadc48ea7cdb0_stdevs_out.tmp","templates_out":"/home/uskhan/anaconda3/envs/mountainlab/mountainsort_examples/bash_examples/001_ms4_bash_example/"/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp"}****
[ Checking process cache ... ]
[ Creating temporary directory ... ]
[ Creating links to input files... ]
[ Preparing temporary outputs... ]
Processing ouput - /home/uskhan/anaconda3/envs/mountainlab/mountainsort_examples/bash_examples/001_ms4_bash_example/"/home/uskhan/anaconda3/envs/mountainlab/tmp"/c3a85fa40a8cb8ca09295f3676bdadc48ea7cdb0_stdevs_out.tmp
false
Processing ouput - /home/uskhan/anaconda3/envs/mountainlab/mountainsort_examples/bash_examples/001_ms4_bash_example/"/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp
false
[ Initializing process ... ]
[ Running ... ] /home/uskhan/anaconda3/envs/mountainlab/etc/mountainlab/packages/qt-mountainview-0.1.4b1/packages/mv/bin/mv.mp mv.mv_compute_templates --_tempdir="/home/uskhan/anaconda3/envs/mountainlab/tmp"/tempdir_7019555dc6_ww3HCK --firings="/home/uskhan/anaconda3/envs/mountainlab/tmp"/tempdir_7019555dc6_ww3HCK/input_firings_8xmie1Gf.mda --timeseries="/home/uskhan/anaconda3/envs/mountainlab/tmp"/tempdir_7019555dc6_ww3HCK/input_timeseries_iUXBUaRz.mda --stdevs_out="/home/uskhan/anaconda3/envs/mountainlab/tmp"/tempdir_7019555dc6_ww3HCK/output_stdevs_out.tmp --templates_out="/home/uskhan/anaconda3/envs/mountainlab/tmp"/tempdir_7019555dc6_ww3HCK/output_templates_out.tmp --clip_size=100
":::: Failed to open diskreadmda file: /home/uskhan/anaconda3/envs/mountainlab/tmp/tempdir_7019555dc6_ww3HCK/input_timeseries_iUXBUaRz.mda"
"File does not exist: /home/uskhan/anaconda3/envs/mountainlab/tmp/tempdir_7019555dc6_ww3HCK/input_timeseries_iUXBUaRz.mda"

[ Removing temporary directory ... ]
Process returned with non-zero exit code.
":::: Failed to open DiskReadMda32 file: "/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp"
"File does not exist: "/home/uskhan/anaconda3/envs/mountainlab/tmp"/87dc91c702cf9bcd62edcded653abaf618b5caa2_templates_out.tmp"
Unable to read chunk of templates in cluster detail view

my mountainlab.env file:
ML_TEMPORARY_DIRECTORY: /home/uskhan/anaconda3/envs/mountainlab/tmp
ML_PACKAGE_SEARCH_DIRECTORY: [default]
ML_ADDITIONAL_PACKAGE_SEARCH_DIRECTORIES: [default]
ML_ADDITIONAL_PRV_SEARCH_DIRECTORIES: [default]
ML_DATABASE_DIRECTORY: [default]

The following are the values actually being used:

Temporary directory: /home/uskhan/anaconda3/envs/mountainlab/tmp
Package search directories: /home/uskhan/anaconda3/envs/mountainlab/etc/mountainlab/packages:/home/uskhan/anaconda3/envs/mountainlab/lib/node_modules/mountainlab/system-packages
PRV search directories: /home/uskhan/anaconda3/envs/mountainlab/tmp
Database directory: /home/uskhan/anaconda3/envs/mountainlab/etc/mountainlab/database

My set-up is: mountainlab-js running on conda 4.7.12 (Python 3.6.9), qt-mountainview-0.1.4b1 compiled with qt 5.9.7, gcc 7.4.0 on Ubuntu 7.4.0-1ubuntu1~18.04.1. I was getting an identical error with a stock build of qt through conda. the new qt-mountainview build is linked correctly in my mountainlab packages/bin directories and references the correct ML_TEMPORARY_DIRECTORY, in my case /home/uskhan/anaconda3/envs/mountainlab/tmp

any help would be appreciated

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