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Cumol/blog 0

Housing my blog cumol.org

Cumol/CaImAn 0

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Cumol/emacs-libvterm 0

Emacs libvterm integration

Cumol/MSstats 0

R package - MSstats

Cumol/org-html-themes 0

How to export Org mode files into awesome HTML in 2 minutes

Cumol/pathtrackr 0

An R package for video tracking and analysing animal movement

Cumol/qmk_firmware 0

Open-source keyboard firmware for Atmel AVR and Arm USB families

Cumol/SAFEclustering 0

SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data

issue openedMouseLand/suite2p

Artefacts in rigid motion correction

In some recent imaging sessions I noticed that I kept getting many ROIs with weird, non-sensical artefacts. They affect a large majority of the ROIs in the image and I didn't understand why I was suddenly getting them. Some example are shown in the red square of the heatmap.

Screenshot from 2020-02-25 18-09-58

I already expected the reason to be the registration. Indeed, the video had movement artefacts, but nothing crazy, some xy shifts here and there. So I decided to manually do the XY-correction with moco (https://github.com/NTCColumbia/moco) and extract the mean fluorescence of some ROIs with Imagej to compare with the suite2p output.

Example 1: A cell where the motion artefacts seem to better than what moco+imagej extracted. cell1 cell1

Example 2: A cell where the motion artefacts are definately still there and more "hacky" compared to moco. cell2-suite2p cell2

Example 3: A cell where the artefacts are very strong in suite2p but less with moco. Additionally, the responses of example 2 and example 3 to be identical (I made sure those were different cells and from two opposite sides of the field of view). Additionally, the imagej trace shows a strong reduction in the fluorescence of the cell while the trace from suite2p does not. This was also confirmed when I examine the video by eye... cell7 cell7

Any idea what is happening here and how I can improve the results?

created time in 9 hours

issue openedjkitchin/scimax

Which package is causing the autocorrection of capital letters?

A tiny detail but an annoying one.

Something is stopping me from writing capital letters. For example, writing K**C**l in a normal org-mode buffer gets immediately turned into K**c**l. The "c" in KCl is supposed to be capital but is turned into lower case. This is usually not so much of a issue, but gets annoying when you want to use the mchecm latex package where $\ce{KCl)$ yields the correct notation while $\ce{Kcl}$ does not.

created time in 17 hours

issue commentjethrokuan/org-roam

Org-roam buffer fails to load

Maybe related but I am not getting an empty org-roam buffer. Completely blank, even though I crated the cache etc.

tpeacock19

comment created time in 5 days

issue commentrailwaycat/homebrew-emacsmacport

emacsclient not functioning correctly

@ylluminarious your fix only solved multiple terminal frames but not the "--create-frame" bug, right?

Not even starting GUI emacs -> "server-start" -> close GUI frame -> emacsclient -c works.

Any idea how to work around this?

jdtsmith

comment created time in 10 days

issue openedjkitchin/scimax

Making scimax quicker?

Inspired by a recent reddit post about the speed of doom emacs, I was wondering if some of the options shipped with doom could also help out startup speed of scimax.

https://github.com/hlissner/doom-emacs/blob/665b627b7c07c8d29ec8d334588cecc2ba308248/docs/faq.org#how-does-doom-start-up-so-quickly

created time in 10 days

issue commentnextcloud/desktop

Desktop Crash Very Occasionally on Long Sync

I am getting this after every transition into the screen saver, for some reason.

benyanke

comment created time in 18 days

issue commentemacs-ess/ESS

running org-babel-execute-src-block no longer produces relevant figure output in session

I also had to look for this and found it in the recent org-mode update.

Its quite a big change for people using source blocks. Should be highlighted better next time.

japhir

comment created time in 22 days

issue commentemacs-helm/helm

How delete all selected buffer from helm-mini by one command?

This is still happening, btw.

helm 20200128.1832

alexei-28

comment created time in 22 days

issue commentkassambara/ggpubr

Please add Tukey post-hoc test to stat_compare_means()

Is there a way to do the same thing with the outputs of glht like so:

stat.test <- aov(len ~ dose, data = df) %>%
  summary(glht(., linfct=mcp(dose="Dunnett")))
BlueCeramicRipples

comment created time in 22 days

fork Cumol/qmk_firmware

Open-source keyboard firmware for Atmel AVR and Arm USB families

https://qmk.fm

fork in 23 days

startedstorax/org-tfl

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issue commentjkitchin/scimax

Latex Export: *Org PDF LaTeX Output* Empty

Does it mean that the function splits the normal Org PDF LaTeX Output into different buffers? I only found makeglossary but no buffer containing the output to debug.

How do you deal with this currently? Do you simply go to the .log file and check there or is there a workaround?

roblem

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startedetterguillaume/CaImDecoding

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issue commentjkitchin/scimax

Latex Export: *Org PDF LaTeX Output* Empty

I have the same issue and it seems to be scimax-specific.

When I export a file (that has some error) using scimax, the buffer is empty. If I export the same file using vanilla emacs, I get a full buffer.

Any idea what is happening here?

roblem

comment created time in a month

pull request commentakermu/emacs-libvterm

Added ubuntu installation notes

It worked for 18.04, haven't tested it on any other system (don't have another machine to test)

On Thu, Jan 23, 2020, 1:39 AM Gabriele Bozzola notifications@github.com wrote:

Does this work on all the different versions of Ubuntu?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/akermu/emacs-libvterm/pull/217?email_source=notifications&email_token=ABFW4FGAPWV5ZI7Z5JFH2ILQ7DRKHA5CNFSM4KJG2LV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJVTXHQ#issuecomment-577452958, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFW4FGDEHMLKTDB2A64CZ3Q7DRKHANCNFSM4KJG2LVQ .

Cumol

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create barnchCumol/org-html-themes

branch : copy-styles-folder-local

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startedfirstcontributions/first-contributions

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PR opened akermu/emacs-libvterm

Added ubuntu installation notes

Added discussions from the following issue https://github.com/akermu/emacs-libvterm/issues/216 to the README file

+20 -0

0 comment

1 changed file

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create barnchCumol/emacs-libvterm

branch : add-ubuntu-installation

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fork Cumol/emacs-libvterm

Emacs libvterm integration

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issue commentakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

I will try this. Since it is my first time, please have patience (but I will manage!) :)

Cumol

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issue commentakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

@Sbozzolo I can do this, but how? Do I simply fork the file?

Cumol

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issue commentjkitchin/scimax

Using scimax with EXWM?

exec emacs in xinitrc is probably where we need to let it know where to find our custom init file.

Need to try that. I remember it being not as straight forward though

Cumol

comment created time in a month

issue openedjkitchin/scimax

Using scimax with EXWM?

Does anyone have experience with using EXWM with the custom init of scimax?

I don't seem to find any information about how to start EXWM when logging into ubuntu with the scimax settings.

created time in a month

issue closedjkitchin/scimax

Results drawer not collapse-able

Using Emacs26 on OSX catalina. Plain emacs allows the collapse of results drawers (from executing a source block), scimax does not.

closed time in a month

Cumol

issue commentjkitchin/scimax

Results drawer not collapse-able

This seems to be something that is connected to my version of emacs used (?). It is still "scimax-specific" but I noticed that it vanished when I switched to another version of emacs on my linux machine (using this PPA https://github.com/kelleyk/ppa-emacs).

Now the behavior is as expected.

Cumol

comment created time in a month

issue closedakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

Maybe a little off-topic, but I am struggling to find out how to install emacs on ubuntu with the modules options.

Can this be done using apt-get or do I have to build emacs from source with the --with-modulesoption?

closed time in a month

Cumol

issue commentakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

Used your suggestion and installed emacs from the ppa. Didn't have to re-link /bin/sh just needed to install libtool and cmake > 3.11 (using brew install cmake).

Cumol

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issue commentakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

Do you think installing it using linuxbrew would also do the trick?

brew install --with-modules emacs

Cumol

comment created time in a month

issue openedakermu/emacs-libvterm

How to build emacs with modules on ubuntu?

Maybe a little off-topic, but I am struggling to find out how to install emacs on ubuntu with the modules options.

Can this be done using apt-get or do I have to build emacs from source with the --with-modulesoption?

created time in a month

issue closedjkitchin/org-ref

Not able to open notes.org file for citation

I am trying to add notes to a citation I have in a file through the menu that pops up when clicking on a citation. However, I keep getting this error:

Org-ref-bib-bibliography-notes is not set to anything

My setup in the user.el file looks like this:

(setq reftex-default-bibliography '("~/ownCloud/phd/papers/bibliography.bib"))
;; *** Org-ref
(setq Org-ref-bibliography-notes "~/ownCloud/phd/papers/notes.org"
      org-ref-default-bibliography '("~/ownCloud/phd/papers/bibliography.bib")
      org-ref-pdf-directory "~/ownCloud/phd/papers/")
;; *** helm-bibtex setup
(setq bibtex-completion-bibliography
      '("~/ownCloud/phd/papers/bibliography.bib"))
(setq bibtex-completion-library-path '("~/ownCloud/phd/papers/"))
(setq bibtex-completion-notes-path "~/ownCloud/phd/papers/notes.org")

I also created the notes.org file thinking that org-ref is not able to create the file.

I have a feeling I am missing something very basic. Any idea what is happening?

A side note, invoking helm-bibtex is not detecting my bibliography file (not showing any entries). Maybe it is a hint

closed time in a month

Cumol
CommitCommentEvent
CommitCommentEvent

issue closedjkitchin/scimax

Generate a TOC of a notebook?

My notebooks contain many org file where each represents an experiment. Each experiment has a title, a subtitle, and a date.

I was wondering if it is possible to somehow generate a table of contents (or a helm popup) for each of the files. Similar to a table of contents with title, subtitle, and date.

Probably something similar to the tag function in the scimax notebook file.

This would make navigating a notebook much easier. Right now, I need to remember what short name I gave each .org file and then look for it when opening a notebook. I usually end up picking the wrong find.

Recently I started to use git-counsel-grep to look for things that I remember typing in the file to find the file. But that is also a mess...

Any idea where to start here?

closed time in a month

Cumol

issue commentjkitchin/scimax

Generate a TOC of a notebook?

Works great!

Which date is it using? I see multiple dates with the "mod" prefix (which I guess means modified).

Cumol

comment created time in a month

issue commentjkitchin/scimax

Generate a TOC of a notebook?

This is exactly what I was looking for.

It chokes on empty .org files (gave me a reason to clean up) but apart from that does it correctly. The columns produced are not well aligned and sorting by date would also be nice. But for not, this is great, thank you!

It could be something that other people might be interested in. Specially if they use scimax and the notebook functionality to write their lab notebooks.

Cumol

comment created time in a month

issue commentjkitchin/scimax

Generate a TOC of a notebook?

Thank you for pointing me towards ivy-org-jump-to-heading-in-directory that is neat but not quite what I envisioned.

instead of headline, it would be nice to get the title as in #+title: <title> of the org file. This would end up with a rather "short" list in comparison to an output with headlines which, as is seen with the above ivy function, a huge list.

Invoking the function would create a helm/ivy buffer with the following:

Title | Date | Link

And choosing one would open that file.

Cumol

comment created time in a month

issue openedjkitchin/scimax

Generate a TOC of a notebook?

My notebooks contain many org file where each represents an experiment. Each experiment has a title, a subtitle, and a date.

I was wondering if it is possible to somehow generate a table of contents (or a helm popup) for each of the files. Similar to a table of contents with title, subtitle, and date.

Probably something similar to the tag function in the scimax notebook file.

This would make navigating a notebook much easier. Right now, I need to remember what short name I gave each .org file and then look for it when opening a notebook. I usually end up picking the wrong find.

Recently I started to use git-counsel-grep to look for things that I remember typing in the file to find the file. But that is also a mess...

Any idea where to start here?

created time in a month

push eventCumol/org-html-themes

Muad Abd El Hay

commit sha 1ebdc4f69dfee03cc5a4eddb10b65102f3e03151

Copying style folder for local theme Adding info about copying the styles folder into the folder of the exported file. This works if exporting a few files residing in a few folders but very tedious for a large number of folders (as is in my case). I tried to adjust the href in the .setup file to make it an absolute path with ~ for home directory, it did not work however. suggestions appreciated.

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fork Cumol/org-html-themes

How to export Org mode files into awesome HTML in 2 minutes

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issue commentjkitchin/scimax

Results drawer not collapse-able

It is assigned to org-cycle, but doing M-x org-cycle on it does not hide the collapse the result (usually an image).

I wonder if it has something to do with images.

Cumol

comment created time in a month

issue closedor/ledger-tools

How to use download-dkb.py?

As I am a python-noob, how do I use this script?

I tried python download-dkb.py and ./download.dkb.py but both give me the following error:

Traceback (most recent call last):
  File "download-dkb.py", line 95, in <module>
    browser, tmp_dir = login(config)
  File "download-dkb.py", line 13, in login
    credentials = load_credentials(config)
  File "/Users/<username>/Desktop/temp/ledger-tools/common.py", line 32, in load_credentials
    output = subprocess.check_output(["gpg", "-q", "-d", config["general"]["key_file"]])
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/configparser.py", line 958, in __getitem__
    raise KeyError(key)
KeyError: 'general'

*replaced my username with <username>

closed time in a month

Cumol

issue commentor/ledger-tools

How to use download-dkb.py?

Solved it. It wasn't using the icsvledgerrc file for some reason. So the import bash script did not work.

If I run it directly from command line like so:

./icsv2ledger/icsv2ledger.py -q -a dkb-giro -c icsv2ledgerrc transaction-history/dkb-giro-2019.csv generated/dkb-giro-2019.ledger

it works fine.

Cumol

comment created time in a month

issue commentor/ledger-tools

How to use download-dkb.py?

Thank you for the help with the date.

However, I have the same exact setup as you and still get the error (and the delimeter is correct).

Any idea what could cause it? I seems like something that has to do with the date

Cumol

comment created time in a month

issue openedleoc/ledgit

no such file /ledgerfiles/assets-dkb.ledger

I am trying to use it to get my transactions from DKB and hitting the following error:

Traceback (most recent call last):
	12: from /Users/muadabdelhay/.ledgit/bin/ledgit:22:in `<main>'
	11: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:19:in `run'
	10: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:19:in `each'
	 9: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:20:in `block in run'
	 8: from /Users/muadabdelhay/.ledgit/lib/handler.rb:101:in `get'
	 7: from /Users/muadabdelhay/.ledgit/lib/handler.rb:101:in `new'
	 6: from /Users/muadabdelhay/.ledgit/lib/handler.rb:9:in `initialize'
	 5: from /Users/muadabdelhay/.ledgit/lib/handler.rb:9:in `new'
	 4: from /Users/muadabdelhay/.ledgit/lib/ledgit/ledger_file.rb:11:in `initialize'
	 3: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1127:in `touch'
	 2: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1127:in `each'
	 1: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1130:in `block in touch'
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1130:in `utime': No such file or directory @ apply2files - /ledgerfiles/assets-dkb.ledger (Errno::ENOENT)
	14: from /Users/muadabdelhay/.ledgit/bin/ledgit:22:in `<main>'
	13: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:19:in `run'
	12: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:19:in `each'
	11: from /Users/muadabdelhay/.ledgit/lib/ledgit.rb:20:in `block in run'
	10: from /Users/muadabdelhay/.ledgit/lib/handler.rb:101:in `get'
	 9: from /Users/muadabdelhay/.ledgit/lib/handler.rb:101:in `new'
	 8: from /Users/muadabdelhay/.ledgit/lib/handler.rb:9:in `initialize'
	 7: from /Users/muadabdelhay/.ledgit/lib/handler.rb:9:in `new'
	 6: from /Users/muadabdelhay/.ledgit/lib/ledgit/ledger_file.rb:11:in `initialize'
	 5: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1127:in `touch'
	 4: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1127:in `each'
	 3: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1129:in `block in touch'
	 2: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1133:in `rescue in block in touch'
	 1: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1133:in `open'
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/fileutils.rb:1133:in `initialize': No such file or directory @ rb_sysopen - /ledgerfiles/assets-dkb.ledger (Errno::ENOENT)

I realize I need to create the ledgerfile but I am have no clue where... I tried putting it in my home directory, the .ledgit directory, but none worked

created time in 2 months

issue commentor/ledger-tools

How to use download-dkb.py?

Using the import-csv-files.sh script requires that the folder generated is already created

Running that script then gives an error when importing the first file:

importing absa-checking-2016...
importing absa-saving-2016...
importing absa-creditcard-2016...
importing dkb-giro-2016...
importing dkb-creditcard-2016...
importing absa-checking-2017...
importing absa-saving-2017...
importing absa-creditcard-2017...
importing dkb-giro-2017...
importing dkb-creditcard-2017...
importing absa-checking-2018...
importing absa-saving-2018...
importing absa-creditcard-2018...
importing dkb-giro-2018...
importing dkb-creditcard-2018...
importing absa-checking-2019...
importing absa-saving-2019...
importing absa-creditcard-2019...
importing dkb-giro-2019...
Traceback (most recent call last):
  File "./icsv2ledger/icsv2ledger.py", line 1057, in <module>
    main(options)
  File "./icsv2ledger/icsv2ledger.py", line 1049, in main
    process_input_output(options.infile, options.outfile)
  File "./icsv2ledger/icsv2ledger.py", line 954, in process_input_output
    for line in  process_csv_lines(csv_lines):
  File "./icsv2ledger/icsv2ledger.py", line 985, in process_csv_lines
    options)
  File "./icsv2ledger/icsv2ledger.py", line 507, in __init__
    entry_date = datetime.strptime(self.date, options.csv_date_format)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/_strptime.py", line 577, in _strptime_datetime
    tt, fraction, gmtoff_fraction = _strptime(data_string, format)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/_strptime.py", line 362, in _strptime
    data_string[found.end():])
ValueError: unconverted data remains: 30.12.2019;"30.12.2019";"Dauerauftrag";">omitted>";"MIETE";"DE68672500201002944932";"SOLADES1HDB";"-390
Cumol

comment created time in 2 months

issue commentor/ledger-tools

How to use download-dkb.py?

Managed to run it and it works fine to download the .csv files automatically. Is there a reason why it only downloads the last 1-2 months of transactions?

Cumol

comment created time in 2 months

issue openedor/ledger-tools

How to use download-dkb.py?

As I am a python-noob, how do I use this script?

I tried python download-dkb.py and ./download.dkb.py but both give me the following error:

Traceback (most recent call last):
  File "download-dkb.py", line 95, in <module>
    browser, tmp_dir = login(config)
  File "download-dkb.py", line 13, in login
    credentials = load_credentials(config)
  File "/Users/<username>/Desktop/temp/ledger-tools/common.py", line 32, in load_credentials
    output = subprocess.check_output(["gpg", "-q", "-d", config["general"]["key_file"]])
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/configparser.py", line 958, in __getitem__
    raise KeyError(key)
KeyError: 'general'

*replaced my username with <username>

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issue commentaertslab/SCopeLoomR

Error adding scenic results

Goes smoothly until the last step (add_senic_regulons) which is the same error.

Error in loom$create_dataset(name = paste0("row_attrs/", key), robj = value,  :
  HDF5-API Errors:
    error #000: ../../../src/H5D.c in H5Dcreate2(): line 147: unable to create dataset
        class: HDF5
        major: Dataset
        minor: Unable to initialize object

    error #001: ../../../src/H5Dint.c in H5D__create_named(): line 494: unable to create and link to dataset
        class: HDF5
        major: Dataset
        minor: Unable to initialize object

    error #002: ../../../src/H5L.c in H5L_link_object(): line 1697: unable to create new link to object
        class: HDF5
        major: Links
        minor: Unable to initialize object

    error #003: ../../../src/H5L.c in H5L_create_real(): line 1941: can't insert link
        class: HDF5
        major: Symbol table
        minor: Unable to insert object

    error #004: ../../../src/H5Gtraverse.c in H5G_traverse(): line 869: internal path traversal failed
        class: HDF5
        major: Symbol table
        minor: Object not found

    error #005: ../../../src/H5Gtraverse.c in H5G_traver
Cumol

comment created time in 3 months

issue commentaertslab/SCopeLoomR

Error adding scenic results

library(SCopeLoomR)

dgem <- exprMat

cell.info <- cellInfo
cell.info$nGene <- colSums(dgem>0)

newembed <- embedding[,c("lvl1","lvl2")]
newembed.name <- "Embedding from Soldatov 2019"

file.name <- "output/mouseNCC-soldatov2019.loom"
loom <- build_loom(file.name=file.name,
                   dgem=dgem,
                   title="Developing mouse NCC data from soldatov 2019",
                   genome="Mouse",
                   default.embedding=newembed,
                   default.embedding.name=newembed.name)

regulonsAUC <- loadInt(scenicOptions, "aucell_regulonAUC")

library(AUCell)

add_scenic_regulons_auc_matrix(loom=loom, regulons.AUC=getAUC(regulonsAUC))

regulons <- readRDS("int/3.1_regulons_forAUCell.Rds")

regulon.enrichment.table <- readRDS("int/2.3_motifEnrichment.Rds")

add_scenic_regulons(loom = loom,regulons = regulons,regulon.enrichment.table = regulon.enrichment.table)
Cumol

comment created time in 3 months

issue openedaertslab/SCopeLoomR

Error adding scenic results

I tried to do this using the export2scope from SCENIC but it didn't work so I decided to go through SCopeLoomR.

Following the vignette, I am getting the following error:

> add_scenic_regulons(loom = loom,regulons = regulons)
Error in loom$create_dataset(name = paste0("row_attrs/", key), robj = value,  : 
  HDF5-API Errors:
    error #000: ../../../src/H5D.c in H5Dcreate2(): line 147: unable to create dataset
        class: HDF5
        major: Dataset
        minor: Unable to initialize object

    error #001: ../../../src/H5Dint.c in H5D__create_named(): line 494: unable to create and link to dataset
        class: HDF5
        major: Dataset
        minor: Unable to initialize object

    error #002: ../../../src/H5L.c in H5L_link_object(): line 1697: unable to create new link to object
        class: HDF5
        major: Links
        minor: Unable to initialize object

    error #003: ../../../src/H5L.c in H5L_create_real(): line 1941: can't insert link
        class: HDF5
        major: Symbol table
        minor: Unable to insert object

    error #004: ../../../src/H5Gtraverse.c in H5G_traverse(): line 869: internal path traversal failed
        class: HDF5
        major: Symbol table
        minor: Object not found

    error #005: ../../../src/H5Gtraverse.c in H5G_traver

created time in 3 months

startedacaccavano/deltaFoF

started time in 3 months

issue openedFafferMcgee/calcium-analysis

Nice package!

Nice package you have there. I put together a similar R package with the same thought behind as I also check for stimuli.

Now I am also motivated to put mine on github!

created time in 3 months

startedFafferMcgee/calcium-analysis

started time in 3 months

startedyu-lab-vt/AQuA

started time in 3 months

startedtbgitoo/calciumImaging

started time in 3 months

issue commentjkitchin/scimax

scimax 3.0?

  1. Making scimax installable with pip is a great advantage. I recently introduced some of my colleagues to emacs and scimax and it is still a relatively steep learning curve. Anything that would make that experience easier is welcome.

  2. I like the idea of making scimax more modular.

I would like to pitch something. It has to do with the thought that scimax can be used to create self-contained publications (or lab notebooks/thesis).

I wonder how one could turn a .org file that contains everything for a paper into one neat package that can be installed on another researchers computer and easily executable. Maybe using docker or singularity? I wonder what is your approach to this and whether it would be something to keep in mind, specially when competing with current solutions for jupyter notebooks etc.

jkitchin

comment created time in 3 months

issue commentaertslab/GENIE3

unable to build a weight matrix on GENIE3

I have a similar problem, but I am limited with the amount of memory I have (60Gb).

I have a 13915x4391 matrix to run GENIE3 on. Is there a way to make it work with the 60Gb of memory that I have? I tried reducing the number of cores used. Started with 30 which gave that error, then I went down to 20 but eventually got the same error.

Any ideas?

juugii

comment created time in 3 months

issue commentjkitchin/scimax

Results drawer not collapse-able

when I press tab, it doesn't. Any idea what I could check to troubleshoot it?

Cumol

comment created time in 4 months

issue openedjkitchin/scimax

Results drawer not collapse-able

Using Emacs26 on OSX catalina. Plain emacs allows the collapse of results drawers (from executing a source block), scimax does not.

created time in 4 months

issue closedMouseLand/suite2p

AttributeError: module '__main__' has no attribute '__file__'

Next error in trying out the newest build. I thought it reminded my of a previous error because it mentions the classifier_user.npy so I copied classifier.npy into the classifier folder and renamed it to classifier_user.npy, but it did not resolve the issue.

Registration metrics, 233.36 sec.
----------- ROI DETECTION AND EXTRACTION
Binning movie in chunks of length 03
Binned movie [3499,516,695], 80.14 sec.
NOTE: estimated spatial scale ~12 pixels, time epochs 2.92, threshold 145.79 
0 ROIs, score=1608.45
Found 281 ROIs, 344.37 sec

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-9-5e74ffea29ef> in <module>
     35 
     36     # run one experiment
---> 37     opsEnd=run_s2p.run_s2p(ops=ops,db=db)

~/Downloads/suite2p/suite2p/run_s2p.py in run_s2p(ops, db)
    253             t11=time.time()
    254             print('----------- ROI DETECTION AND EXTRACTION')
--> 255             ops1[ipl] = extract.detect_and_extract(ops1[ipl])
    256             ops = ops1[ipl]
    257             fpath = ops['save_path']

~/Downloads/suite2p/suite2p/extract/extract.py in detect_and_extract(ops)
     98     ### apply default classifier ###
     99     if len(stat) > 0:
--> 100         classfile = os.path.join(os.path.abspath(os.path.dirname(__main__.__file__)),
    101             "classifiers/classifier_user.npy",
    102         )

AttributeError: module '__main__' has no attribute '__file__'



closed time in 4 months

Cumol

issue commentMouseLand/suite2p

AttributeError: module '__main__' has no attribute '__file__'

Okay, I just installed the pip version and now it is running again...

Cumol

comment created time in 4 months

issue commentjkitchin/scimax

Fresh install of emacs throws exception of missing diminish package

The problem is probably related to this here and it suggests going down to an older TLS version

jboes

comment created time in 5 months

issue commentAlexEMG/DeepLabCut

ERROR:root:Cannot activate multiple GUI eventloops

This actually worked, as only option. Thank you.

Do you think that it would make sense to file an issue on the jupyter page?

Cumol

comment created time in 5 months

issue commentAlexEMG/DeepLabCut

ERROR:root:Cannot activate multiple GUI eventloops

Forced it with the suggested code and switched to WXAgg Still the same error

Cumol

comment created time in 5 months

issue commentAlexEMG/DeepLabCut

ERROR:root:Cannot activate multiple GUI eventloops

Could it be that some paranthesis were missing? I ran the following:

import matplotlib
gui_env = ['TKAgg','GTKAgg','Qt4Agg','WXAgg']
for gui in gui_env:
    try:
        print ("testing", gui)
        matplotlib.use(gui,warn=False, force=True)
        from matplotlib import pyplot as plt
        break
    except:
        continue
print ("Using:",matplotlib.get_backend())

with this output

testing TKAgg
Using: TkAgg
Cumol

comment created time in 5 months

issue openedAlexEMG/DeepLabCut

ERROR:root:Cannot activate multiple GUI eventloops

Describe the bug basically the same situation as with this issue: https://github.com/AlexEMG/DeepLabCut/issues/124

To Reproduce

  1. run deeplabcut on videos (works)
  2. extract frames (works)
  3. run the following:
%gui wx
deeplabcut.refine_labels(path_config)

Expected behavior Expected is a popup of a GUI to correct the frames. It worked the first time I ran the notebook and the first time when I reboot the machine.

Desktop (please complete the following information about your system):

  • OS: Ubuntu 18.04
  • DeepLabCut Version: 2.0.6.3
  • Browser: Firefox

Additional context As stated above. It always works the first time after a fresh reboot. It does not work after restarting the kernel or terminating all processes and starting again.

created time in 5 months

issue commentjolars/eulerr

Error in `fit_diagram()`: `!any(combinations < 0) is not TRUE`

Found the error. I was supplying a dataframe instead of a matrix...

jolars

comment created time in 5 months

issue commentjolars/eulerr

Error in `fit_diagram()`: `!any(combinations < 0) is not TRUE`

I am not getting this particular error but other weird behavior. Opening a new issue for that.

jolars

comment created time in 5 months

issue commentdanielfm/spotify.el

Couldn't connect =\

I am getting this error even though spotify_oauth2_callback_server.py is in my path

guilhermecomum

comment created time in 5 months

issue commentMouseLand/suite2p

AttributeError: module '__main__' has no attribute '__file__'

Same error on a windows machine running a fresh install.

Cumol

comment created time in 5 months

issue commentjkitchin/scimax

Fresh install of emacs throws exception of missing diminish package

Emacs 26.3 and Ubuntu 18.04

jboes

comment created time in 5 months

startedkushalkolar/MESmerize

started time in 5 months

issue commentjkitchin/scimax

Fresh install of emacs throws exception of missing diminish package

I am still getting a diminish-related error when doing a fresh install package-compute-transaction: Package ‘diminish-’ is unavailable

jboes

comment created time in 5 months

issue openedMouseLand/suite2p

AttributeError: module '__main__' has no attribute '__file__'

Next error in trying out the newest build. I thought it reminded my of a previous error because it mentions the classifier_user.npy so I copied classifier.npy into the classifier folder and renamed it to classifier_user.npy, but it did not resolve the issue.

Registration metrics, 233.36 sec.
----------- ROI DETECTION AND EXTRACTION
Binning movie in chunks of length 03
Binned movie [3499,516,695], 80.14 sec.
NOTE: estimated spatial scale ~12 pixels, time epochs 2.92, threshold 145.79 
0 ROIs, score=1608.45
Found 281 ROIs, 344.37 sec

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-9-5e74ffea29ef> in <module>
     35 
     36     # run one experiment
---> 37     opsEnd=run_s2p.run_s2p(ops=ops,db=db)

~/Downloads/suite2p/suite2p/run_s2p.py in run_s2p(ops, db)
    253             t11=time.time()
    254             print('----------- ROI DETECTION AND EXTRACTION')
--> 255             ops1[ipl] = extract.detect_and_extract(ops1[ipl])
    256             ops = ops1[ipl]
    257             fpath = ops['save_path']

~/Downloads/suite2p/suite2p/extract/extract.py in detect_and_extract(ops)
     98     ### apply default classifier ###
     99     if len(stat) > 0:
--> 100         classfile = os.path.join(os.path.abspath(os.path.dirname(__main__.__file__)),
    101             "classifiers/classifier_user.npy",
    102         )

AttributeError: module '__main__' has no attribute '__file__'



created time in 5 months

issue openedstencila/encoda

Support for org-mode

When thinking about executable documents, aside from jupyter notebooks, org-mode pops to mind.

org-mode is an emacs mode that allows writing simple text documents with code blocks (from any language), execute them, and embed the results in the same file. John Kitchin (https://github.com/jkitchin) and his group have used org-mode with this functionality to write and publish more than 20 papers (http://kitchingroup.cheme.cmu.edu/scimax).

There are already well established (built in) converters to latex and html. Additionally, using pandoc (which supports org-mode), the documents can be converted to a myriad of other outputs.

Maybe it would be a good addition to the list.

created time in 5 months

issue closedMouseLand/suite2p

KeyError: 'badframes'

Updated everything to newest github version and getting the following error:

FOUND OPS IN /home/generalubuntu/mnt/Muad/ca-imaging/exp164-20190626/1drg-on/suite2p/plane0
** Found 10500 tifs - converting to binary **
800 frames of binary, time 90.87 sec.
1600 frames of binary, time 205.09 sec.
2400 frames of binary, time 316.45 sec.
3200 frames of binary, time 430.30 sec.
4000 frames of binary, time 543.19 sec.
4800 frames of binary, time 652.84 sec.
5600 frames of binary, time 763.69 sec.
6400 frames of binary, time 873.31 sec.
7200 frames of binary, time 979.14 sec.
8000 frames of binary, time 1089.90 sec.
8800 frames of binary, time 1197.45 sec.
9600 frames of binary, time 1304.87 sec.
10400 frames of binary, time 1412.46 sec.
time 1428.32 sec. Wrote tifs to binaries for 1 planes
SKIPPING REGISTRATION FOR ALL PLANES...
NOTE: binary file created, but registration not performed
>>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-5-5e74ffea29ef> in <module>
     35 
     36     # run one experiment
---> 37     opsEnd=run_s2p.run_s2p(ops=ops,db=db)

~/Downloads/suite2p/suite2p/run_s2p.py in run_s2p(ops, db)
    242             if do_regmetrics and ops1[ipl]['nframes']>=1500:
    243                 t0=time.time()
--> 244                 ops1[ipl] = metrics.get_pc_metrics(ops1[ipl])
    245                 print('Registration metrics, %0.2f sec.'%(time.time()-t0))
    246                 np.save(os.path.join(ops1[ipl]['save_path'],'ops.npy'), ops1[ipl])

~/Downloads/suite2p/suite2p/register/metrics.py in get_pc_metrics(ops, use_red)
    154         mov  = sample_frames(ops, ix, ops['reg_file_chan2'])
    155     else:
--> 156         mov  = sample_frames(ops, ix, ops['reg_file'])
    157 
    158     pclow, pchigh, sv, v = pclowhigh(mov, nlowhigh, nPC)

~/Downloads/suite2p/suite2p/utils.py in sample_frames(ops, ix, reg_file, crop)
    150             frames x Ly x Lx
    151     """
--> 152     bad_frames = ops['badframes']
    153     ix = ix[bad_frames[ix]==0]
    154     Ly = ops['Ly']

KeyError: 'badframes'

Might be related to https://github.com/MouseLand/suite2p/issues/181

closed time in 5 months

Cumol

issue commentMouseLand/suite2p

KeyError: 'badframes'

Resolved by deleting the already present suite2p folder and starting fresh. It does seem to be connected with re-running the pipeline on already present data.

Cumol

comment created time in 5 months

issue openedMouseLand/suite2p

KeyError: 'badframes'

Updated everything to newest github version and getting the following error:

FOUND OPS IN /home/generalubuntu/mnt/Muad/ca-imaging/exp164-20190626/1drg-on/suite2p/plane0
** Found 10500 tifs - converting to binary **
800 frames of binary, time 90.87 sec.
1600 frames of binary, time 205.09 sec.
2400 frames of binary, time 316.45 sec.
3200 frames of binary, time 430.30 sec.
4000 frames of binary, time 543.19 sec.
4800 frames of binary, time 652.84 sec.
5600 frames of binary, time 763.69 sec.
6400 frames of binary, time 873.31 sec.
7200 frames of binary, time 979.14 sec.
8000 frames of binary, time 1089.90 sec.
8800 frames of binary, time 1197.45 sec.
9600 frames of binary, time 1304.87 sec.
10400 frames of binary, time 1412.46 sec.
time 1428.32 sec. Wrote tifs to binaries for 1 planes
SKIPPING REGISTRATION FOR ALL PLANES...
NOTE: binary file created, but registration not performed
>>>>>>>>>>>>>>>>>>>>> PLANE 0 <<<<<<<<<<<<<<<<<<<<<<

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-5-5e74ffea29ef> in <module>
     35 
     36     # run one experiment
---> 37     opsEnd=run_s2p.run_s2p(ops=ops,db=db)

~/Downloads/suite2p/suite2p/run_s2p.py in run_s2p(ops, db)
    242             if do_regmetrics and ops1[ipl]['nframes']>=1500:
    243                 t0=time.time()
--> 244                 ops1[ipl] = metrics.get_pc_metrics(ops1[ipl])
    245                 print('Registration metrics, %0.2f sec.'%(time.time()-t0))
    246                 np.save(os.path.join(ops1[ipl]['save_path'],'ops.npy'), ops1[ipl])

~/Downloads/suite2p/suite2p/register/metrics.py in get_pc_metrics(ops, use_red)
    154         mov  = sample_frames(ops, ix, ops['reg_file_chan2'])
    155     else:
--> 156         mov  = sample_frames(ops, ix, ops['reg_file'])
    157 
    158     pclow, pchigh, sv, v = pclowhigh(mov, nlowhigh, nPC)

~/Downloads/suite2p/suite2p/utils.py in sample_frames(ops, ix, reg_file, crop)
    150             frames x Ly x Lx
    151     """
--> 152     bad_frames = ops['badframes']
    153     ix = ix[bad_frames[ix]==0]
    154     Ly = ops['Ly']

KeyError: 'badframes'

Might be related to https://github.com/MouseLand/suite2p/issues/181

created time in 5 months

issue commentMouseLand/suite2p

Extract fluorescence from second channel?

any idea what I could try?

Is there a way to extract the ROIs as files readable by the ImageJ ROI manager?

Cumol

comment created time in 5 months

issue commentMouseLand/suite2p

Critical parameter/s for Cell detection (ops0.sig in MATLAB)

Pressing Alt+enter after marking two overlapping cells produces this message in the terminal computing automated merge suggestions... but nothing seems to happens.

Pressing Alt+enter again gives this error:

Traceback (most recent call last):
  File "/home/muad/Downloads/suite2p/suite2p/gui/gui2p.py", line 291, in keyPressEvent
    merge.merge_cells(self)
AttributeError: module 'suite2p.gui.merge' has no attribute 'merge_cells'


PhantomSpike

comment created time in 5 months

issue commentMouseLand/suite2p

Critical parameter/s for Cell detection (ops0.sig in MATLAB)

Just noticed that. Playing around with it now.

When I click on a cell, the view is centered and zoomed on it. is it intended behavior?

PhantomSpike

comment created time in 5 months

issue commentMouseLand/suite2p

Critical parameter/s for Cell detection (ops0.sig in MATLAB)

Pressing Alt+enter does not do anything. There is also no "Merge ROIs" tab. Am I missing something? I am on the sparse-mode branch

PhantomSpike

comment created time in 5 months

issue commentMouseLand/suite2p

Extract fluorescence from second channel?

Same problem. I also changed the "nchannel" argument to "2" because I thought that this would be the problem. did not help.

Maybe I am supplying the path of the red channel in a wrong format?

Cumol

comment created time in 5 months

IssuesEvent

issue commentMouseLand/suite2p

Extract fluorescence from second channel?

Got to try this and getting an error: This is the code I am using. It is originally from a loop to run multiple files. I am feeding it only one folder though.

import glob, os
from natsort import natsorted
import imghdr

froot = ['/home/generalubuntu/mnt/Muad/ca-imaging/exp164-20190626/1drg-on/']
ops['meanImg_chan2'] = '/home/generalubuntu/mnt/Muad/ca-imaging/exp164-20190626/1drg-on/tdtomato/red.tif'



for fri in froot:
    
    files = glob.glob(os.path.join(fri, "*.*"))
    condition = np.empty(len(files))
    for i, name in enumerate(files):
        condition[i] = imghdr.what(files[i]) == 'tiff'
    files = np.extract(condition,files)
    files = natsorted(files)
    for n,f in enumerate(files):
        files[n] = os.path.basename(f)

    db = {
          'h5py': [], # a single h5 file path
          'h5py_key': 'data',
          'look_one_level_down': False, # whether to look in ALL subfolders when searching for tiffs
          'data_path': [fri], 
                                # a list of folders with tiffs 
                                # (or folder of folders with tiffs if look_one_level_down is True, or subfolders is not empty)

          'subfolders': [], # choose subfolders of 'data_path' to look in (optional)
          'tiff_list': files # list of tiffs in folder * data_path *!
        }
    
    
    
    # run one experiment
    opsEnd=run_s2p.run_s2p(ops=ops,db=db)

The error I am getting is the following:

/home/generalubuntu/mnt/Muad/ca-imaging/exp164-20190626/1drg-on/suite2p/plane0
found binaries
/home/generalubuntu/suite2p/plane0/data.bin
skipping registration...
[6 6]
nt0=10
(1050, 516, 695)
spatial scale 3, time epochs 1.00, threshold 60.00 
0 0.03669571876525879 1503.2659912109375
200 21.48070764541626 255.8083038330078
394 32.10496187210083 0.0
time 82.4969. Found 394 ROIs
extracted 1000/10500 frames in 9.87 sec
extracted 6000/10500 frames in 63.47 sec
extracted 10500/10500 frames in 115.98 sec
extracted 10500/10500 frames in 115.99 sec
time 214.6798. Extracted fluorescence from 394 ROIs

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-12-103a141b93bc> in <module>
     36 
     37     # run one experiment
---> 38     opsEnd=run_s2p.run_s2p(ops=ops,db=db)

~/Downloads/suite2p-test/suite2p/suite2p/run_s2p.py in run_s2p(ops, db)
    205             roidetect = True
    206         if roidetect:
--> 207             ops1[ipl] = utils.get_cells(ops1[ipl])
    208             ops = ops1[ipl]
    209             fpath = ops['save_path']

~/Downloads/suite2p-test/suite2p/suite2p/utils.py in get_cells(ops)
    651         if 'chan2_thres' not in ops:
    652             ops['chan2_thres'] = 0.65
--> 653         ops, redcell = chan2detect.detect(ops, stat)
    654         np.save(os.path.join(fpath, 'redcell.npy'), redcell)
    655         np.save(os.path.join(fpath, 'F_chan2.npy'), F_chan2)

~/Downloads/suite2p-test/suite2p/suite2p/chan2detect.py in detect(ops, stat)
     49     #ops2 = ops.copy()
     50     mimg = ops['meanImg'].copy()
---> 51     mimg2 = ops['meanImg_chan2'].copy()
     52 
     53     # subtract bleedthrough of green into red channel

AttributeError: 'str' object has no attribute 'copy'

Any idea what is happening?

Cumol

comment created time in 6 months

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