Differences between RTF and ODF transformation

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iandol
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Joined: Fri Jan 25, 2008 2:31 pm

Differences between RTF and ODF transformation

Post by iandol »

Hi, I wanted to use the [ citation modifier to replace () with [], and it didn't work in my ODF (I possibly don't understand what it is supposed to do). I made two test files (Libreoffice 4.3.2.2 and Textedit from Yosemite GM) from the text below to try the different modifiers and in the process realised there are a couple of differences when I process my test file as an RTF or as an ODF (J Neurophysiol format). See the screenshot ODF on the left, RTF on the right.
Screen Shot 2014-10-04 at 14.58.41.jpg
Screen Shot 2014-10-04 at 14.58.41.jpg (209.2 KiB) Viewed 9273 times
There are differences for both * and ! — and neither RTF or ODF does what I would like when using [ — my ideal replacement is [Bastos et al. 2012].

My test text:

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This is a new test to see {Bastos et al., 2012, #95736} what gets entered?

Creating removable in-text citations !
This is a new test to see {!Bastos et al., 2012, #95736} what gets entered?

Change parentheses to square brackets [
This is a new test to see {[Bastos et al., 2012, #95736} what gets entered?

Excluding enclosing punctuation in a final citation *
This is a new test to see {*Bastos et al., 2012, #95736} what gets entered?

Replace temporary in-text citations with date only %
This is a new test to see {%Bastos et al., 2012, #95736} what gets entered?

Excluding author and title in the final citation &
This is a new test to see {&Bastos et al., 2012, #95736} what gets entered?

Placing the author in front of the citation ^
This is a new test to see {^Bastos et al., 2012, #95736} what gets entered?

Eliminate authors from final citation -
This is a new test to see {-Bastos et al., 2012, #95736} what gets entered?

Cited Pages
This is a new test to see {Bastos et al., 2012, #95736@697} what gets entered?

Mixing literal (quoted) text with temporary in-text citations \ \
This is a new test to see {\some text here: \Bastos et al., 2012, #95736} what gets entered? 
Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

The [ changes only parentheses that are generated as part of the footnote to [ ]. I has no effect on what encloses the final citation (that's determined by the format settings).

I'll look at the other two examples you posted.

Jon
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Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

I see and have fixed the problem with *. I can't reproduce the problem with !.

Jon
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iandol
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Re: Differences between RTF and ODF transformation

Post by iandol »

It is still reproducible with ! here with j neurophysiol, here is the ref itself if that makes a difference:

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[{"dateAdded":"3491311623.000000","dateModified":"3491311623.000000","location":"Center for Neuroscience, University of California, Davis, Davis, CA 95618 USA; Center for Mind and Brain, University of California, Davis, Davis, CA 95618 USA; Ernst Strungmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, Deutschordenstrasse 46, 60528 Frankfurt, Germany.","volume":"76(4)","keywords":"theoretical model\ncanonical microcircuit\npredictive coding\nperceptual inference\nbayesian brain\nintrinsic connx\ninterlaminar\nfeedback\nforward v backward\ngamma","uuid":"E2F0D7B8-44BC-4E27-B11C-387D2B523382","url":"http://www.ncbi.nlm.nih.gov/pubmed/23177956","user15":"Neuron","type":"9","dateRecordUpdated":"3491311623.000000","journal":"Neuron","user17":"10.1016/j.neuron.2012.10.038","VarCharField":"\t3491311623\t","rating":"0","uniqueID":"95736","pages":"695-711","authors":"Bastos, A. M.\nUsrey, W. M.\nAdams, R. A.\nMangun, G. R.\nFries, P.\nFriston, K. J.","thedate":"2012 Nov 21","title":"Canonical microcircuits for predictive coding","user6":"1097-4199 (Electronic)\r0896-6273 (Linking)","abstract":"This Perspective considers the influential notion of a canonical (cortical) microcircuit in light of recent theories about neuronal processing. Specifically, we conciliate quantitative studies of microcircuitry and the functional logic of neuronal computations. We revisit the established idea that message passing among hierarchical cortical areas implements a form of Bayesian inference-paying careful attention to the implications for intrinsic connections among neuronal populations. By deriving canonical forms for these computations, one can associate specific neuronal populations with specific computational roles. This analysis discloses a remarkable correspondence between the microcircuitry of the cortical column and the connectivity implied by predictive coding. Furthermore, it provides some intuitive insights into the functional asymmetries between feedforward and feedback connections and the characteristic frequencies over which they operate.","user18":"23177956","notes":"Bastos, Andre M\nUsrey, W Martin\nAdams, Rick A\nMangun, George R\nFries, Pascal\nFriston, Karl J\neng\nEY013588/EY/NEI NIH HHS/\nMH055714/MH/NIMH NIH HHS/\nR01 EY013588/EY/NEI NIH HHS/\nWellcome Trust/United Kingdom\nResearch Support, N.I.H., Extramural\nResearch Support, Non-U.S. Gov't\nResearch Support, U.S. Gov't, Non-P.H.S.\nReview\n2012/11/28 06:00\nNeuron. 2012 Nov 21;76(4):695-711. doi: 10.1016/j.neuron.2012.10.038."}]
and the odt is attached...
Attachments
test.odt.zip
(32.77 KiB) Downloaded 240 times
Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

Your file works just fine here -- the ! citation is removed after the scan. Try again when the next update of Bookends is released and see if you still have a problem with this.

Jon
Sonny Software
iandol
Posts: 465
Joined: Fri Jan 25, 2008 2:31 pm

Re: Differences between RTF and ODF transformation

Post by iandol »

Thanks Jon! Completely offtopic but on Yosemite public beta 5 I see the following messages in console:

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08/10/2014 09:42:56.216 Bookends[356]: WARNING: The Gestalt selector gestaltSystemVersion is returning 10.9.0 instead of 10.10.0. Use NSProcessInfo's operatingSystemVersion property to get correct system version number.
Call location:
08/10/2014 09:42:56.219 Bookends[356]: 0   CarbonCore                          0x9a6827e7 ___Gestalt_SystemVersion_block_invoke + 135
08/10/2014 09:42:56.219 Bookends[356]: 1   libdispatch.dylib                   0x939df0b5 dispatch_once_f + 251
08/10/2014 09:42:56.220 Bookends[356]: 2   libdispatch.dylib                   0x939e00d8 dispatch_once + 31
08/10/2014 09:42:56.220 Bookends[356]: 3   CarbonCore                          0x9a614fb8 _Gestalt_SystemVersion + 1050
08/10/2014 09:42:56.220 Bookends[356]: 4   CarbonCore                          0x9a614b69 Gestalt + 150
08/10/2014 09:42:56.220 Bookends[356]: 5   rbframework.dylib                   0x027bdd64 RuntimeDebugMemoryUsed + 16948
08/10/2014 09:42:56.220 Bookends[356]: 6   rbframework.dylib                   0x027a3724 RuntimeInit + 84
08/10/2014 09:42:57.562 Bookends[356]: plugin 'BookendsFramework.framework' failed to load: dlopen(/Applications/Bookends.app/Contents/Frameworks/BookendsFramework.framework, 0): no suitable image found.  Did find:
	/Applications/Bookends.app/Contents/Frameworks/BookendsFramework.framework: not a file
08/10/2014 09:42:57.657 Bookends[356]: objc[356]: Class QTMovieLayer is implemented in both /System/Library/Frameworks/QTKit.framework/Versions/A/QTKit and /Applications/Bookends.app/Contents/Frameworks/dtPlugins.rbx_0.dylib. One of the two will be used. Which one is undefined.
08/10/2014 09:42:57.657 Bookends[356]: objc[356]: Class QTMovie is implemented in both /System/Library/Frameworks/QTKit.framework/Versions/A/QTKit and /Applications/Bookends.app/Contents/Frameworks/dtPlugins.rbx_0.dylib. One of the two will be used. Which one is undefined.
08/10/2014 09:42:58.049 Bookends[356]: plugin 'YAJL.framework' failed to load: dlopen(/Applications/Bookends.app/Contents/Frameworks/YAJL.framework, 0): no suitable image found.  Did find:
	/Applications/Bookends.app/Contents/Frameworks/YAJL.framework: not a file
08/10/2014 09:42:58.050 Bookends[356]: plugin 'yaz.framework' failed to load: dlopen(/Applications/Bookends.app/Contents/Frameworks/yaz.framework, 0): no suitable image found.  Did find:
	/Applications/Bookends.app/Contents/Frameworks/yaz.framework: not a file
Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

You'll see something similar in any release of OS X. Don't worry about the log, the messages aren't significant.

Jon
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iandol
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Joined: Fri Jan 25, 2008 2:31 pm

Re: Differences between RTF and ODF transformation

Post by iandol »

I'm also seeing problems with using {\ \} with ODT files. Please find a test.odt with a bookends export attached (I tried using APA 6th Edition and several others without difference). The raw text is:

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The interaction between a focussed central and surrounding regions of visual space has been conceived in terms of a ‘classical’ receptive field {\CRF; \ Hartline, 1940, #437; Kuffler, 1953 #418;Barlow, 1953 #413;Hubel, 1962 #440}, in which visual stimulation elicits direct neural firing (ON, OFF or mixed sign); and an ‘extended’ modulatory surrounding area {\extra-classical receptive field, ECRF; \ Allman, 1985 #1109}, that cannot by itself drive the cell to fire. 
The Hartline and Allman citation fail to convert:

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The interaction between a focussed central and surrounding regions of visual space has been conceived in terms of a ‘classical’ receptive field (\CRF; \ Hartline, 1940, #437; Kuffler, 1953; Barlow, 1953; Hubel & Wiesel, 1962), in which visual stimulation elicits direct neural firing (ON, OFF or mixed sign); and an ‘extended’ modulatory surrounding area (\extra-classical receptive field, ECRF; \ Allman, 1985 #1109), that cannot by itself drive the cell to fire. 


Barlow, H. B. (1953). Summation and inhibition in the frog’s retina. The Journal of Physiology, 119(1), 69-88. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=13035718
Hubel, D. H., & Wiesel, T. N. (1962). Receptive fields, binocular interaction and functional architecture in the cat’s visual cortex. The Journal of Physiology, 160(1), 106-154. Retrieved from http://jp.physoc.org
Kuffler, S. W. (1953). Discharge Patterns and Functional Organization of Mammalian Retina. The Journal of Neurophysiology, 16(1), 37-68. Retrieved from http://jn.physiology.org
They are fine with the same text saved as an RTF...
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Test.zip
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Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

I'm very surprised you say that works with RTF. Assuming you're using ; as a citation delimiter, your temp citation makes no sense. It's used for "literal text" before or after a citation (see the user guide). In your first citation, I suspect you mean

{\CRF \Hartline, 1940, #437; Kuffler, 1953 #418;Barlow, 1953 #413;Hubel, 1962 #440}

This citation works in an .odt file as expected in my tests.

Jon
Sonny Software
iandol
Posts: 465
Joined: Fri Jan 25, 2008 2:31 pm

Re: Differences between RTF and ODF transformation

Post by iandol »

Ah, I assumed all characters within the \ \ were escaped, thus ; could be used as it is for the RTF. Is there a way to escape the characters within \ \ or can you allow \ \ to automatically escape all characters within?

This is the correctly formatted RTF output:

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The interaction between a focussed central and surrounding regions of visual space has been conceived in terms of a ‘classical’ receptive field (CRF; Hartline, 1940; Kuffler, 1953; Barlow, 1953; Hubel & Wiesel, 1962), in which visual stimulation elicits direct neural firing (ON, OFF or mixed sign); and an ‘extended’ modulatory surrounding area (extra-classical receptive field, ECRF; Allman et al., 1985), that cannot by itself drive the cell to fire. 

...correct bibliography here...
Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

All characters are "escaped" except the citation separator -- it's not possible to do that. But there is no need, because it appears that you're using the ; in the FINAL citation to separate references. So just make the literal text it's own "citation":

{\CRF \; Hartline, 1940, #437; Kuffler, 1953 #418;Barlow, 1953 #413;Hubel, 1962 #440}

Jon
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iandol
Posts: 465
Joined: Fri Jan 25, 2008 2:31 pm

Re: Differences between RTF and ODF transformation

Post by iandol »

Yes, that sounds fine, thanks Jon! I'll wait for the next version and hopefully my other RTF vs. ODT issues will shake themselves out...
Last edited by iandol on Mon Oct 13, 2014 11:48 pm, edited 1 time in total.
iandol
Posts: 465
Joined: Fri Jan 25, 2008 2:31 pm

Re: Differences between RTF and ODF transformation

Post by iandol »

Actually it doesn't work, I get the following:

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{\CRF\; Hartline, 1940, #437; Kuffler, 1953 #418;Barlow, 1953 #413;Hubel, 1962 #440}
becomes:

Code: Select all

(\CRF\; Hartline, 1940; Barlow, 1953; Kuffler, 1953; Hubel & Wiesel, 1962)
The \ \ are left in the final text...
Jon
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Re: Differences between RTF and ODF transformation

Post by Jon »

I can't say why it's not working for you, that example works for me. This is a tech support issue and doesn't belong on the forum. If you want to follow up, please contact tech support directly (support@sonnysoftware.com).

Jon
Sonny Software
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