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Web-based tools for collecting, analyzing, and sharing data from a DIY spectrometer

Home Page: http://spectralworkbench.org

License: GNU General Public License v3.0

Ruby 48.30% JavaScript 9.99% CSS 2.97% HTML 37.87% Shell 0.49% Dockerfile 0.33% Makefile 0.05%

hacktoberfest

spectral-workbench's Issues

major improvements to graph zooming/cropping interface

could also use tags to refer to start:234 end:565 but this issue is mainly about the live interface to explore data. is flot good enough? D3?

D3 has this great interface: http://bl.ocks.org/mbostock/1667367

create "subtract spectrum" button

which also creates a tag link like #40

dropdown nav menu doesn't work on Opera for android

Fix for opera? http://stackoverflow.com/questions/14244357/twitter-bootstrap-dropdown-links-not-working-on-mobile

didn't work. try newer version of Bootstrap v2.x

create repository of tagged wavelengths for known points like 694nm (chromium)

and let people share them at spectralworkbench.org/macro/gemstones or something, or /app/foo

suggested by mr hans kok

bulk image download

Presently the way to download the raw image data is one at a time using the format http://spectralworkbench.org/system/photos/<id>/original/capture.png. If the format is wrong, the filename is in the metadata for each spectrum.

If a bulk download of 60+ images is required for offline processing experiments, iterating this format will be a major strain on the server. Worse yet would be if the data wasn't downloaded, so that each experimental modification required a new download of 60+ images.

Desired is a system which will gather the raw images for a set of spectrum ids submit by the user. The backend will grab the images, compress them, and send them to the user in a single push.

For all images ever, it might be good if we back up the images to S3, DropBox, or some photo sharing site. Many external services have a bulk download button which does the process of compressing a large set of files and sending them as a single file to the user. This would certainly eliminate effort on our part.

I don't think S3 has that capability built in by default, but it will statically host files. Monthly caches could be put there, but that feels far too arbitrary.

close "More tools" dialog after selection

/capture doesn't sample from the middle by default

at startup in the settings menu, if no cross-section is selected and I just click "Begin Capturing" I do not see the middle cross section when I start capturing.

There should be a default cross section-- and I remember there being one before... seems like a new problem.

shift to amazon s3-based storage

can't apply existing calibration to spectra

when I click on the "copy this calibration" button nothing happens in chrome.

assortment of auto-assistance and labeling

show cross-section line on analysis page, w/ "change this" edit btn
display clipping warning on analysis page

Offline Use/RasPi Image

This gizmo is small enough that it would be useful in field camps where there is no internet connectivity. Making available a RaspberryPi image that permitted "off-line" usage with possibly a locally stored database of popular exaple spectrograms would greatly improve the usefuleness of this appliance

reset graph colors when switching back from RGB mode

assume this is in Analyze page, but @mkoistinen may correct me

should offer 'autodetection' of brightest row in capture interface

in settings screen but also if you see nothing in your video output

index should not return data, but there should be equivalent call

Presently, if one calls http://spectralworkbench.org?format=xml, all the spectra (possibly truncated at some arbitrary point) are returned with metadata and spetrum data.

spectral-workbench/webserver/app/controllers/spectrums_controller.rb

Lines 12 to 31 in 3902e7d

 def index 

 if logged_in? 

 redirect_to "/dashboard" 

 else 

 @spectrums = Spectrum.find(:all,:order => "created_at DESC", :conditions => ["author != 'anonymous'"], :limit => 100) 

 @spectrums = @spectrums.paginate :page => params[:page], :per_page => 24 

 # @anon_spectrums = Spectrum.find(:all,:order => "created_at DESC", :conditions => {:author => "anonymous"}) 

 # @anon_spectrums = @anon_spectrums.paginate :page => params[:page], :per_page => 4 

 @sets = SpectraSet.find(:all,:limit => 4,:order => "created_at DESC") 

 @comments = Comment.all :limit => 12, :order => "id DESC" 

 respond_to do |format| 

 format.html { 

 render :template => "spectrums/index.html.erb" 

 } # show.html.erb 

 format.xml { render :xml => @spectrums } 

 end 

 end 

 end

The index should contain just enough to decide which spectra to download without including the actual spectrum data. This is more friendly to front-end javascript decision making, but can also by used by offline massive processing applications.

There should be a similar call, however, which returns all the metadata and the spectral data. The concept is that the front end javascript has decided which spectra to grab, and will now make this new call to get it. So it'll also need some selectors, minimally a set of ids will suffice.

Possibly this interface could be called bulk or bulkdata.

Additionally, index and bulk should support csv and json on top of html and xml..

recent calibrations not available to capture interface

We should have a button that lets you choose a recent calibration, in the /capture interface. It should show an up-to-date list of recent calibrations, ajaxly in case the capture page hasn't been reloaded
We should have the button turn red when a new calibration is detected, via 10-sec AJAX polling, and display an alert that a new calibration is available with a button to use it.

can't use "more tools" after saving a set

after I save a set I no longer have access to the "more tools" pallette. I'd like to create a set adn then equalize the area underneath the spectra for purposes of comparison. To do that I have to re-build the set, adding in each of the spectra again.

I wish I could just apply transforms to saved sets.

finish upgrading to Rails 3 conventions

Deprecated session secret setting
Previously, session secret was set directly on ActionController::Base; it's now config.secret_token.
More information: http://lindsaar.net/2010/4/7/rails_3_session_secret_and_session_store

The culprits: 
    - config/initializers/session_store.rb

Deprecated test_help path
You now must require 'rails/test_help' not just 'test_help'.
More information: http://weblog.rubyonrails.org/2009/9/1/gem-packaging-best-practices

The culprits: 
    - test/test_helper.rb

Soon-to-be-deprecated ActiveRecord calls
Methods such as find(:all), find(:first), finds with conditions, and the :joins option will soon be deprecated.
More information: http://m.onkey.org/2010/1/22/active-record-query-interface

The culprits: 
    - app/models/processed_spectrum.rb
    - app/models/spectrum.rb
    - app/controllers/spectrums_controller.rb
    - app/models/processed_spectrum.rb
    - app/models/spectrum.rb
    - app/models/user.rb
    - app/controllers/spectrums_controller.rb
    - app/controllers/likes_controller.rb

Deprecated ActionMailer API
You're using the old ActionMailer API to send e-mails in a controller, model, or observer.
More information: http://lindsaar.net/2010/1/26/new-actionmailer-api-in-rails-3

The culprits: 
    - app/models/spectrum.rb
    - app/models/spectra_set.rb
    - app/models/user.rb
    - app/controllers/users_controller.rb
    - app/controllers/sets_controller.rb
    - app/controllers/comments_controller.rb

Old ActionMailer class API
You're using the old API in a mailer class.
More information: http://lindsaar.net/2010/1/26/new-actionmailer-api-in-rails-3

The culprits: 
    - app/models/user_mailer.rb
    - app/models/user_mailer.rb

design UI for wavelength range limiting

The current version of Spectralworkbench is hard-coded to display reflectance spectra between 250 and 800nm. Since the webcam is sensitive past 800nm, could you add functionality in the UI to extend this display to spectra beyond 800nm (say 850nm or so)?

Thanks! -david mccloskey

prompt to reload if new calibration becomes available (changed)

this involves making the differences between logged-in and non-logged-in interfaces solely javascript-based; no erb template conditionals. And a $W.analyze.toggleLoggedIn() call to switch them over. Maybe .logged-in and .logged-out classes?

update/re-add user unit tests around OpenID auth

Since migrating to rails 3 and ditching our previous authentication library, user unit testing is failing pretty hard. Run rake test to try it out.

accept or modify non-latin characters

These upload, but they don't save properly in the db.

downloadable data for whole sets

This should be possible via XML/JSON pretty easily.

store image captured and additional details in localstorage in offline mode

offer to upload when reconnected. @Sreyanth - I remember you had some part of this working, right?

improve CSV format consistency and standards-compliance

The CSV download of a spectrum is two (unlabeled) columns. I presume this is only the spectral data.

For JSON, XML, and HTML, the full set of metadata and data is included.

One issue that needs to be addressed is that the spectral data is always returned as embedded JSON (e.g. in XML it is <data>{ json stuff }</data>).

The current format returned by the CSV is a good start towards demuxing the JSON into CSV, but we need to append/prepend the rest of the metadata as well as provide column names.

Addendum by @jywarren: include FWHM values in CSV; details in jywarren#137

Support open standards for exporting spectra

Because open data and portability are good things(TM), we probably want to support open standards for this sort of data. The custom exports that currently exist certainly work, but might not be as portable or as easy to work with as open standards.

We might want to export some small amount of metadata regarding ownership and licensing for each spectra which I don't think is part of any standard.

enable markdown in comments

intermittent trouble with "set sample row"

@Fastie sez:

I just hit a spell when I couldn't "set sample row" and got the "Something went wrong." I tried many times on two different spectra and tried re-extracting from photo without success. I think things started working again when I tried "Detect brightest row." Afterwards, everything was fine. The offending spectra were http://spectralworkbench.org/analyze/spectrum/4514 and 4515

combined flipping issues, recent calibration not loading in capture

we experienced briefly (and undocumented) a problem when using a flipped spectra in the capture interface for calibration.

we were also were unable to get the capture spectra to calibrate

fix flot label styling

spectra calibrated with a macro do not get tagged "calibrated"

@Fastie sez:

Spectra calibrated with a macro ($w.calibrate(...)) never show up as a choice for calibrating while uploading or from the analyze page. This means that it is not possible to use some well-calibrated spectra for calibration. The macro feature offers a workaround, but it would be nice to calibrate on upload using a spectrum carefully calibrated with a macro.

offer helpful suggestions on spectra tagged "CFL"

move auto-calibration code into production, refine interface

building on @Sreyanth's work

search function should search tags too

mobile selection of cross section does not show data in live graph during capture

I have attached two screenshots from my Galaxy Note 3 smartphone. I am using the smartphone DIY instructions and the back facing camera. I found first that the online spectralworkbench utility does not work with both Chrome (back facing camera only displays 'black' with nothing covering camera!) and Opera. I can only use it properly with current Firefox. The screenshots come from the DIY spec/smartphone pointed at a perfectly white display on a 12" tablet. Why when I perform the capture does NOTHING SHOW UP! I have also tried to point it at a compact fluorescent, but same thing happens. What am I doing wrong?
Thank you,
Jason

spectra appear in wrong place when comparing

In doing a comparison, the 20W-50 spectra is offset by 100nm.

Upon saving the set it appears in the right place.

refresh graph on window resize

better guidance for avoiding clipping and overexposure

This is a complex UI question as well as a technical/hardware one.

cross-section start/end powertagging

We have a terminology collision here; extraction in spectroscopy can refer to extracting something from a sample with solvents. But what I mean here is a means, like Infragrammar (http://publiclab.org/wiki/infragrammar), to specify how data should be taken from an image.

Another collision is "recipes" -- here I mean like a parseable expression, but in #64 "recipes" refers to something different; the steps in an experimental method. The feature in this issue needs renaming.

This could include start/end pixels for a cross section, whether to take the average or sum of the pixel color values, etc.

The recipe might be stored as a tag, such as start:151,355, end:454,1266 and rgb:average or rgb:sum

presumably we'd have to enforce certain rules for namespaces like rgb: or start: -- maybe most recent wins; also, when you add such tags, it should enter the changes in a log

commenting on specific wavelengths/annotating graphs

$("#placeholder").bind("plotclick", function (event, pos, item) {
  alert("You clicked at " + pos.x + ", " + pos.y);
  // axis coordinates for other axes, if present, are in pos.x2, pos.x3, ...
  // if you need global screen coordinates, they are pos.pageX, pos.pageY

  if (item) {
    highlight(item.series, item.datapoint);
    alert("You clicked a point!");
  }
});

Currently wavenumbers and wavelength are used as units. Sometimes eV are needed as well as a unit. It would be great to have that as an option for the x axis; the conversion is: eV = 1239.82/wavelength

http://edgeguides.rubyonrails.org/upgrading_ruby_on_rails.html

use tags to refer to calibration or absorption sources

subtract-from:<id> and calibrated-from:<id>

Clicking on such tags would go to the source, not a listing of that tag.

	def index
	if logged_in?
	redirect_to "/dashboard"
	else
	@spectrums = Spectrum.find(:all,:order => "created_at DESC", :conditions => ["author != 'anonymous'"], :limit => 100)
	@spectrums = @spectrums.paginate :page => params[:page], :per_page => 24

	# @anon_spectrums = Spectrum.find(:all,:order => "created_at DESC", :conditions => {:author => "anonymous"})
	# @anon_spectrums = @anon_spectrums.paginate :page => params[:page], :per_page => 4
	@sets = SpectraSet.find(:all,:limit => 4,:order => "created_at DESC")
	@comments = Comment.all :limit => 12, :order => "id DESC"

	respond_to do \|format\|
	format.html {
	render :template => "spectrums/index.html.erb"
	} # show.html.erb
	format.xml { render :xml => @spectrums }
	end
	end
	end

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spectral-workbench's Issues

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