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Luke Tuite
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Luke Tuite
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added mne.py to generate uuids for swcs
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‎ingest/migrations/0016_swc_swc_uuid.py‎

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# Generated by Django 3.2.18 on 2023-06-06 15:44
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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('ingest', '0015_swc'),
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]
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operations = [
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migrations.AddField(
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model_name='swc',
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name='swc_uuid',
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field=models.CharField(max_length=1000, null=True),
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),
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]

‎ingest/mne.py‎

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#---------------------------
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# Based on this system:
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# http://gurno.com/adam/mne/
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#---------------------------
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class Mne:
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def num_to_mne(num):
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dataa= [
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"zip", "ace", "act", "add", "age",
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"aim", "air", "and", "ant", "ape",
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"arm", "art", "ash", "ask", "bad",
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"bag", "ban", "bar", "bat", "bay",
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"bed", "bet", "bid", "big", "bin",
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"bit", "bog", "boo", "box", "bud",
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"bug", "bun", "bus", "cab", "can",
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"cap", "car", "cat", "cop", "cot",
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"cow", "cry", "cub", "cup", "cut",
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"day", "den", "did", "die", "dig",
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"dim", "dip", "dog", "dry", "dub",
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"dud", "dug", "ear", "eat", "eel",
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"egg", "elf", "elk", "elm", "end",
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"fan", "far", "fat", "fed", "few",
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"fib", "fig", "fin", "fit", "fix",
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"fly", "fog", "foo", "fox", "fry",
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"fun", "gab", "gag", "gap", "gas",
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"gel", "gem", "get", "gin", "got",
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"gum", "gut", "had", "has", "hat",
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"hen", "hex", "hid", "hip", "hit",
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"hog", "hop", "hot", "how", "hub",
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"hug", "hum", "hut", "ice", "ill",
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"imp", "ink", "irk", "jab", "jam",
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"jar", "jaw", "jet", "jig", "job",
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"jog", "jot", "joy", "key", "kid",
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"kin", "kit", "lab", "lag", "lap",
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"law", "lax", "lay", "leg", "let",
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"lid", "lip", "lit", "lot", "low",
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"mad", "map", "mat", "men", "met",
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"mix", "mob", "moo", "mop", "mud",
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"mug", "nab", "nag", "nap", "net",
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"new", "nil", "nip", "nod", "nor",
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"now", "nut", "oak", "oat", "odd",
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"off", "old", "orb", "out", "owl",
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"own", "pad", "pal", "pan", "pay",
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"pen", "pet", "pie", "pig", "pin",
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"pit", "ply", "pod", "pop", "pot",
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"pox", "pry", "pun", "pup", "put",
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"rag", "ran", "rat", "raw", "red",
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"rid", "rig", "rip", "rot", "row",
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"rub", "rug", "run", "rut", "rye",
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"sad", "sag", "sap", "sat", "saw",
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"say", "set", "shy", "sip", "sit",
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"ski", "sky", "sly", "sob", "soy",
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"spa", "spy", "tab", "tag", "tan",
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"tap", "tar", "tax", "the", "tie",
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"tin", "tip", "top", "toy", "try",
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"tub", "tug", "use", "van", "vat",
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"vex", "vow", "wag", "war", "was",
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"wax", "web", "wet", "who", "wig",
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"win", "wit", "yes", "yet", "zoo",
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"all"]
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#-----------------------------------
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#store 256 decoded elements in stack
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#-----------------------------------
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stack=[]
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#print("NUM=",num)
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q=num
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if q < 256 :
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q,r = divmod(num,256)
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stack.append(r)
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#print(q,r)
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else:
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while q > 255 :
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q,r = divmod(q,256)
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stack.append(r)
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#print(q,r)
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#q,r = divmod(q,256)
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stack.append(q)
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#print(q,r)
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#else:
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#print(len(stack))
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#----------------------
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#Finally code the stack
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#----------------------
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rstring=""
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first=True
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for element in reversed(stack):
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if first:
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first=False
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else:
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rstring=rstring + '-'
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rstring=rstring+dataa[element]
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#print ("R:",stack)
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return rstring
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def mne_to_num(mme):
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datad= {
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"zip" : "000", "ace" : "001", "act" : "002", "add" : "003", "age" : "004",
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"aim" : "005", "air" : "006", "and" : "007", "ant" : "008", "ape" : "009",
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"arm" : "010", "art" : "011", "ash" : "012", "ask" : "013", "bad" : "014",
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"bag" : "015", "ban" : "016", "bar" : "017", "bat" : "018", "bay" : "019",
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"bed" : "020", "bet" : "021", "bid" : "022", "big" : "023", "bin" : "024",
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"bit" : "025", "bog" : "026", "boo" : "027", "box" : "028", "bud" : "029",
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"bug" : "030", "bun" : "031", "bus" : "032", "cab" : "033", "can" : "034",
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"cap" : "035", "car" : "036", "cat" : "037", "cop" : "038", "cot" : "039",
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"cow" : "040", "cry" : "041", "cub" : "042", "cup" : "043", "cut" : "044",
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"day" : "045", "den" : "046", "did" : "047", "die" : "048", "dig" : "049",
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"dim" : "050", "dip" : "051", "dog" : "052", "dry" : "053", "dub" : "054",
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"dud" : "055", "dug" : "056", "ear" : "057", "eat" : "058", "eel" : "059",
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"egg" : "060", "elf" : "061", "elk" : "062", "elm" : "063", "end" : "064",
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"fan" : "065", "far" : "066", "fat" : "067", "fed" : "068", "few" : "069",
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"fib" : "070", "fig" : "071", "fin" : "072", "fit" : "073", "fix" : "074",
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"fly" : "075", "fog" : "076", "foo" : "077", "fox" : "078", "fry" : "079",
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"fun" : "080", "gab" : "081", "gag" : "082", "gap" : "083", "gas" : "084",
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"gel" : "085", "gem" : "086", "get" : "087", "gin" : "088", "got" : "089",
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"gum" : "090", "gut" : "091", "had" : "092", "has" : "093", "hat" : "094",
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"hen" : "095", "hex" : "096", "hid" : "097", "hip" : "098", "hit" : "099",
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"hog" : "100", "hop" : "101", "hot" : "102", "how" : "103", "hub" : "104",
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"hug" : "105", "hum" : "106", "hut" : "107", "ice" : "108", "ill" : "109",
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"imp" : "110", "ink" : "111", "irk" : "112", "jab" : "113", "jam" : "114",
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"jar" : "115", "jaw" : "116", "jet" : "117", "jig" : "118", "job" : "119",
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"jog" : "120", "jot" : "121", "joy" : "122", "key" : "123", "kid" : "124",
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"kin" : "125", "kit" : "126", "lab" : "127", "lag" : "128", "lap" : "129",
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"law" : "130", "lax" : "131", "lay" : "132", "leg" : "133", "let" : "134",
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"lid" : "135", "lip" : "136", "lit" : "137", "lot" : "138", "low" : "139",
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"mad" : "140", "map" : "141", "mat" : "142", "men" : "143", "met" : "144",
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"mix" : "145", "mob" : "146", "moo" : "147", "mop" : "148", "mud" : "149",
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"mug" : "150", "nab" : "151", "nag" : "152", "nap" : "153", "net" : "154",
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"new" : "155", "nil" : "156", "nip" : "157", "nod" : "158", "nor" : "159",
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"now" : "160", "nut" : "161", "oak" : "162", "oat" : "163", "odd" : "164",
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"off" : "165", "old" : "166", "orb" : "167", "out" : "168", "owl" : "169",
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"own" : "170", "pad" : "171", "pal" : "172", "pan" : "173", "pay" : "174",
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"pen" : "175", "pet" : "176", "pie" : "177", "pig" : "178", "pin" : "179",
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"pit" : "180", "ply" : "181", "pod" : "182", "pop" : "183", "pot" : "184",
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"pox" : "185", "pry" : "186", "pun" : "187", "pup" : "188", "put" : "189",
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"rag" : "190", "ran" : "191", "rat" : "192", "raw" : "193", "red" : "194",
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"rid" : "195", "rig" : "196", "rip" : "197", "rot" : "198", "row" : "199",
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"rub" : "200", "rug" : "201", "run" : "202", "rut" : "203", "rye" : "204",
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"sad" : "205", "sag" : "206", "sap" : "207", "sat" : "208", "saw" : "209",
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"say" : "210", "set" : "211", "shy" : "212", "sip" : "213", "sit" : "214",
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"ski" : "215", "sky" : "216", "sly" : "217", "sob" : "218", "soy" : "219",
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"spa" : "220", "spy" : "221", "tab" : "222", "tag" : "223", "tan" : "224",
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"tap" : "225", "tar" : "226", "tax" : "227", "the" : "228", "tie" : "229",
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"tin" : "230", "tip" : "231", "top" : "232", "toy" : "233", "try" : "234",
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"tub" : "235", "tug" : "236", "use" : "237", "van" : "238", "vat" : "239",
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"vex" : "240", "vow" : "241", "wag" : "242", "war" : "243", "was" : "244",
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"wax" : "245", "web" : "246", "wet" : "247", "who" : "248", "wig" : "249",
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"win" : "250", "wit" : "251", "yes" : "252", "yet" : "253", "zoo" : "254",
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"all" : "255" }
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stack=[]
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values=mme.split('-')
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#lookup numbers and put on stack
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for i in values:
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stack.append(int(datad[i]))
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#print("F:",stack)
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vsum=0
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value=0
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for i in range(0,len(stack)-1,1):
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#print ("Stack[",i,"]: ", stack[i])
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#print("len(stack)-i-1: ",len(stack)-i-1)
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vsum=256**(len(stack)-i-1) * stack[i] + vsum
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#vsum=value
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#if stack[i]==0 :
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#else:
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# value=(256**(pwr)) * stack[i]
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#vsum=vsum+value
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#print (i,vsum)
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#print("Stack length=",len(stack))
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vsum=vsum+stack[len(stack)-1]
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#print("Final VSUM: ",vsum)
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return(vsum)
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def mne_test(self):
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#Simple Test code for MNE:
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mne = Mne()
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testvalues=[5,255,256,257,511,512,513,65535,65536,65537,16777215,16777216,16777217]
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for i in testvalues:
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vv=self.num_to_mne(i)
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print("Coding: ", i, vv)
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print("Deconding: ",vv, mne.mne_to_num(vv))
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‎ingest/models.py‎

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Original file line numberDiff line numberDiff line change
@@ -448,5 +448,6 @@ class SWC(models.Model):
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segmentTags = models.CharField(max_length=256, blank=True, null=True)
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proofreadingLevel = models.CharField(max_length=256, blank=True, null=True)
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notes = models.TextField()
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swc_uuid = models.CharField(max_length = 1000, blank=False, null=True)
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data_set = models.ForeignKey(Dataset, on_delete=models.SET_NULL, blank=True, null=True)
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sheet = models.ForeignKey(Sheet, on_delete=models.SET_NULL, blank=True, null=True)

‎ingest/templates/ingest/swc_detail.html‎

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@@ -19,6 +19,7 @@ <h3>SWC</h3>
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<th>segmentTags</th>
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<th>proofreadingLevel</th>
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<th>notes</th>
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<th>swc_uuid</th>
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</tr>
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</thead>
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<tbody>
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<td>{{ s.segmentTags }}</td>
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<td>{{ s.proofreadingLevel }}</td>
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<td>{{ s.notes }}</td>
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<td>{{s.swc_uuid}}</td>
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</tr>
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{% endfor %}
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</table>

‎ingest/views.py‎

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@@ -24,6 +24,7 @@
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from celery.result import AsyncResult
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from . import tasks
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from .mne import Mne
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from .field_list import required_metadata
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from .filters import CollectionFilter
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from .forms import CollectionForm, ImageMetadataForm, DescriptiveMetadataForm, UploadForm, collection_send
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notes = s['notes']
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swc = SWC(tracingFile=tracingFile, sourceData=sourceData, sourceDataSample=sourceDataSample, sourceDataSubmission=sourceDataSubmission, coordinates=coordinates, coordinatesRegistration=coordinatesRegistration, brainRegion=brainRegion, brainRegionAtlas=brainRegionAtlas, brainRegionAtlasName=brainRegionAtlasName, brainRegionAxonalProjection=brainRegionAxonalProjection, brainRegionDendriticProjection=brainRegionDendriticProjection, neuronType=neuronType, segmentTags=segmentTags, proofreadingLevel=proofreadingLevel, notes=notes, data_set_id=data_set_id,sheet_id=sheet.id)
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swc.save()
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swc_no_uuid = swc.save()
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print(swc_no_uuid.id)
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swc_uuid = Mne.num_to_mne(swc_no_uuid.id)
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print(swc_uuid)
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this_swc = SWC.objects.get(id=swc_no_uuid.id)
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# this_swc(swc_uuid=swc_uuid)
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# this_swc.save()
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return True
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except Exception as e:
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print(repr(e))

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