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Neural-Systems-at-UIO / LocaliZoom

Localizoom viewer https://localizoom.readthedocs.io
MIT License
3 stars 1 forks source link

Updated merger with new atlas links don't work #8

Closed Majpuc closed 4 years ago

Majpuc commented 4 years ago

Apparently the atlas is not recognized... says "undefined"

http://cmbn-navigator.uio.no/navigator/filmstripzoom/filmstripzoom.html?atlas=undefined&series=5255&preview=WHSRatv2Preview.png

I have used an xml from QNII anchored to WHSv2 named "H441_TimmThionin_horizontal_IR_gjeldende_US" located here: X:\hbp-02421\0000_FINAL-Timm-Thionin\H441\QNII_anchoring

Tevemadar commented 4 years ago

Applied a fix with the new assumption that N3 expects "Short atlas name" from https://github.com/Neural-Systems-at-UIO/Navigator/wiki/Atlas-naming-convention

Majpuc commented 4 years ago

Still "undefined" in the atlas field e.g. H441a

Tevemadar commented 4 years ago

Navigator bug. Manually modified 841_2785_5255_H441a_Timm_dark_horizontal_s001 (first section in H441a) to v2, and then it opened (single-section LZ). Let @darwinjob know.

darwinjob commented 4 years ago

Applied a fix with the new assumption that N3 expects "Short atlas name" from https://github.com/Neural-Systems-at-UIO/Navigator/wiki/Atlas-naming-convention

I don't like assumptions :) I believed we have agreed on the short atlas names, haven't we? @Tevemadar what did you expect/prefer? We still can change this...

Tevemadar commented 4 years ago

@darwinjob short atlas names are fine with me. From the top of my head I'm not sure if it has been discussed what anchored_to field will contain after the update.

darwinjob commented 4 years ago

Navigator bug. Manually modified 841_2785_5255_H441a_Timm_dark_horizontal_s001 (first section in H441a) to v2, and then it opened (single-section LZ). Let @darwinjob know.

Apparently N3 generates LZ links with "undefined" if the atlas is WHS Rat v3. If I manually set the id to 200100 everything works http://cmbn-navigator.uio.no/navigator/filmstripzoom/filmstripzoom.html?atlas=200100&series=5255&preview=WHSRatv2Preview.png It's a typo :) somewhere, should be easy to fix.

darwinjob commented 4 years ago

@darwinjob short atlas names are fine with me. From the top of my head I'm not sure if it has been discussed what anchored_to field will contain after the update.

I made the changes in https://github.com/Neural-Systems-at-UIO/Navigator/wiki/Atlas-naming-convention BTW how do I allow others to edit the table in this GitHub of yours ;) ?

darwinjob commented 4 years ago

@Tevemadar I've fixed this here: meta.innerHTML=ouv.name+"<br>"+cfg.Width.toString()+" x "+cfg.Height.toString()+"<br>" +JSON.parse('{"100000":"ABA Mouse CCFv2","200000":"WHS Rat v2","300000":"ABA Mouse CCFv3_2015", "300100":"ABA Mouse CCFv3_2017", "200100":"WHS Rat v3"}')[args.atlas] +"<br><a href='http://cmbn-navigator.uio.no/navigator/feeder/original/?id="+section_id+"' target='_blank'>Download image</a>"; meta.style.left=window.innerWidth-meta.scrollWidth-5+"px";

What's about this one?

function meshview(){ var wnd=window.open("about:blank","meshview"); var d=wnd.document; d.write("<html><head><title>MeshView export</title><style>textarea{width:100%;height:80%}</style></head><body>"); d.write("Please copy the coordinates below into <a href='http://www.nesys.uio.no/MeshGen/MeshView.html?bitlas=" +JSON.parse('{"100000":"ABAMouseHier","200000":"WHSRatV2","300000":"ABAv3-Hier"}')[args.atlas] +".bitlas' target='_blank'>MeshView</a>. Viewer needs Adobe Flash."); if(args.atlas==="100000")d.write("<br>(Hint: \"Basic cell groups and regions\" is the gray wrapper structure to be switched off)"); if(args.atlas==="300000")d.write("<br>(Hint: \"root\" is the gray wrapper structure to be switched off)"); d.write("<textarea id='ta'>"); d.write("RGB 0 0 1\n"); d.write("SCALE 5"); switch(args.atlas){ case "200000": case "300000": meshmarkers.forEach(function(item){ d.write("\n"+item.x.toFixed(0)+" "+item.y.toFixed(0)+" "+item.z.toFixed(0)); }); break; case "100000": meshmarkers.forEach(function(item){ d.write("\n"+item.x.toFixed(0)+" "+(item.y-528).toFixed(0)+" "+(item.z-320).toFixed(0)); }); } d.write("</textarea></body></html>"); d.close(); }

Pff, why the markup is ruined??

Tevemadar commented 4 years ago

@darwinjob Cool, LZ in Navigator is properly updated then. MeshView export is for the Flash-based MeshView, which has no updated atlases, and the identifiers are the ones which are in the code. So exporting will need a larger rework in order to point to the new version.

While this editor does not show it, markdown for multiline code blocks is to prepend them by four spaces. The backquotes thing makes format inline and drops the whitespace.

`multiline block
with spaces in front`

The same without spaces (linebreak disappears, backquotes are consumed for the code-formatting itself):

multiline block without spaces in front

Majpuc commented 4 years ago

Still not working... @Tevemadar can you have a look at these two links: http://cmbn-navigator.uio.no/navigator/filmstripzoom/filmstripzoom.html?atlas=undefined&series=5256&preview=WHSRatv2Preview.png http://cmbn-navigator.uio.no/navigator/filmstripzoom/filmstripzoom.html?atlas=undefined&series=5255&preview=WHSRatv2Preview.png

darwinjob commented 4 years ago

Yeah, I’m on it, I just need to deploy the new version. This requires a restart but we have a teaching session taking place.

Majpuc commented 4 years ago

Hi Dmitri,

Okay, thanks!

Maja ☺

darwinjob commented 4 years ago

Fixed

Majpuc commented 3 years ago

Validated 24.09.2020