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VirtualFlyBrain / VFB_json_schema

VFB json schema spec + code for rolling queries producing VFB json schema + related integration tests
Apache License 2.0
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Templates not returning own channel image #8

Closed Robbie1977 closed 5 years ago

Robbie1977 commented 5 years ago

I suggest splitting after template: https://github.com/VirtualFlyBrain/VFB_json_schema/blob/master/src/query_roller.py#L49

"(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->" \

to

"(channel:Individual)-[irw:in_register_with]->(template:Individual) OPTIONAL MATCH (template)-[:depicts]->" \

this avoid the query returning nothing because 'primary' and 'template_anat' are the same node.

dosumis commented 5 years ago

Odd that the loop-back doesn't fix this. Seems cypher doesn't like having two edges in a pattern matching the same edge.

This is surprisingly hard to fix, given the structure of queries and how JSON is rolled. We may need a special category for Templates.

Robbie1977 commented 5 years ago

I think it's just a cypher excentricity that is doesn't follow edges it's already crossed/included - probably to prevent infinite looping.

Robbie1977 commented 5 years ago

A special Query for Templates may not be a bad idea in general anyway

Robbie1977 commented 5 years ago

Another reason for the Template is the need to return results for all domains

Robbie1977 commented 5 years ago

Current JSON created at terminfo loading of template for domains and image data then loaded by stack viewer:

{  
    "indexNumber":0,
    "serverUrl":"https://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi",
    "fileLocation":"/disk/data/VFB/IMAGE_DATA/VFB/i/0001/7894//volume.wlz",
    "subDomains":[ 
        [ $(Voxel Size) ],
        [ $(Domain VFBid) ],
        [ $(label - for floatover) ],
        [ $(Domain ClassId) ],
        [ $(centre point "[x,y,z]") ]
    ]
}

Note: subDomains list index = domain index.

Full version for JFRC2:

{  
    "indexNumber":0,
    "serverUrl":"https://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi",
    "fileLocation":"/disk/data/VFB/IMAGE_DATA/VFB/i/0001/7894//volume.wlz",
    "subDomains":[  
        [  
            "0.62208",
            "0.62208",
            "0.62208",
            null
        ],
        [  
            "VFB_00017894",
            null,
            "VFB_00030621",
            "VFB_00030622",
            "VFB_00030609",
            "VFB_00030625",
            "VFB_00030619",
            "VFB_00030900",
            "VFB_00030605",
            "VFB_00030600",
            "VFB_00030602",
            "VFB_00030613",
            "VFB_00030617",
            "VFB_00030616",
            "VFB_00030631",
            "VFB_00030615",
            "VFB_00030606",
            "VFB_00030901",
            "VFB_00030902",
            "VFB_00030903",
            "VFB_00030620",
            null,
            "VFB_00030612",
            "VFB_00030611",
            "VFB_00030629",
            "VFB_00030624",
            "VFB_00030633",
            "VFB_00030623",
            "VFB_00030628",
            "VFB_00030614",
            "VFB_00030608",
            "VFB_00030632",
            "VFB_00030626",
            "VFB_00030630",
            "VFB_00030627",
            "VFB_00030610",
            "VFB_00030838",
            "VFB_00030601",
            "VFB_00030603",
            "VFB_00030618",
            "VFB_00030599",
            null,
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            "VFB_00030840",
            "VFB_00030604",
            "VFB_00030607",
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            "VFB_00030866",
            "VFB_00030867",
            "VFB_00030868",
            "VFB_00030869",
            "VFB_00030870",
            "VFB_00030871",
            "VFB_00030872",
            "VFB_00030873",
            "VFB_00030874",
            "VFB_00030875",
            "VFB_00030876",
            "VFB_00030877",
            "VFB_00030878",
            "VFB_00030879",
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        ],
        [  
            "adult brain",
            null,
            "accessory medulla",
            "lobula",
            "nodulus",
            "bulb",
            "protocerebral bridge",
            "lateral horn",
            "lateral accessory lobe",
            "saddle",
            "cantle",
            "antennal mechanosensory and motor center",
            "inferior clamp",
            "vest",
            "inferior bridge",
            "antler",
            "crepine",
            "pedunculus of adult mushroom body",
            "vertical lobe of adult mushroom body",
            "medial lobe of adult mushroom body",
            "flange",
            null,
            "lobula plate",
            "ellipsoid body",
            "adult antennal lobe",
            "medulla",
            "fan-shaped body",
            "superior lateral protocerebrum",
            "superior intermediate protocerebrum",
            "superior medial protocerebrum",
            "anterior ventrolateral protocerebrum",
            "posterior ventrolateral protocerebrum",
            "wedge",
            "posterior lateral protocerebrum",
            "anterior optic tubercle",
            "gorget",
            "calyx of adult mushroom body",
            "superior posterior slope",
            "inferior posterior slope",
            "superior clamp",
            "epaulette",
            null,
            null,
            null,
            null,
            null,
            null,
            null,
            null,
            "adult gnathal ganglion",
            "prow",
            "gall",
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            "adult cerebral ganglion",
            "adult subesophageal zone",
            "adult central complex",
            "adult mushroom body",
            "inferior neuropils",
            "lateral complex",
            "adult optic lobe",
            "superior neuropils",
            "ventrolateral neuropils",
            "ventromedial neuropils",
            "central body",
            "lobe system of adult mushroom body",
            "clamp",
            "lobula complex",
            "ventrolateral protocerebrum",
            "posterior slope",
            "ventral complex",
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            "FBbt_00003701",
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dosumis commented 5 years ago

From discussion in dev meeting . it seems there are two issue here:

  1. Retrieving image of template when rolling TermInfo for a template.
  2. Getting all information about a template needed to run 2 and 3D viewers.

These should have separate schemas (cc @Robbie1977)

For second use case - I have started a new ticket #16

dosumis commented 5 years ago

I believe this is all fixed (mostly on linked ticket) so closing.