restructured project. working on slab stitching

X_A_584665.txt

@@ -0,0 +1,4 @@
+1	0	1	-0.959367110826	-0.282159267106	0.000000000000	0.282159126230	-0.959368030311	0.000000000000				/nobackup/flyTEM/spark_montage/test/EXP_v12_SURF_montage_1_4/scale_0.15/layer_images/1.0.png	-999
+2	0	1	-0.959367110826	-0.282159267106	0.000000000000	0.282159126230	-0.959368030311	0.000000000000				/nobackup/flyTEM/spark_montage/test/EXP_v12_SURF_montage_1_4/scale_0.15/layer_images/2.0.png	-999
+3	0	1	-0.959367110826	-0.282159267106	0.000000000000	0.282159126230	-0.959368030311	0.000000000000				/nobackup/flyTEM/spark_montage/test/EXP_v12_SURF_montage_1_4/scale_0.15/layer_images/3.0.png	-999
+4	0	1	-0.959367110826	-0.282159267106	0.000000000000	0.282159126230	-0.959368030311	0.000000000000				/nobackup/flyTEM/spark_montage/test/EXP_v12_SURF_montage_1_4/scale_0.15/layer_images/4.0.png	-999

classes/@tile/tile.m

@@ -265,7 +265,11 @@
                 im = get_image_renderer(obj, 1.0, 'true');
             end
         end
-
+        function url = get_url(obj)
+            % returns the Renderer URL to be consumed by the Renderer service API
+            url = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
+                obj.server, obj.owner, obj.project, obj.stack, obj.renderer_id);
+        end
         function im = show(obj, filter)
             if nargin<2, filter = 'true';end
             warning off;

data_exchange/append_renderer_stack.m

@@ -38,7 +38,7 @@
 
 if strfind(resp, 'caught exception'),
     disp(resp);
-    error('append_renderer_stack: server-side error reported');
+    error('append_renderer_stack: server reported error');
 end
 
 
@@ -50,6 +50,7 @@
 
 %%
 function check_input(rc, rc_base, fn, MET_format)
+if stack_complete(rc), disp(rc);error('The stack is in state: COMPLETE');end
 if ~isfield(rc, 'baseURL'), disp_usage; error('baseURL not provided');end
 if ~isfield(rc, 'owner'), disp_usage; error('owner not provided');end
 if ~isfield(rc, 'project'), disp_usage; error('project not provided');end

data_exchange/ingest_section_into_renderer_database.m

@@ -36,4 +36,4 @@ function ingest_section_into_renderer_database(mL,rc_target, rc_base, dir_work)
 end
 
 %% complete stack
-resp = renderer_stack_state_complete(rc);
+resp = renderer_stack_state_complete(rc_target);

external/JSON.m

@@ -0,0 +1,267 @@
+classdef JSON < handle
+    % v = JSON.parse(jsonString) converts a JSON string to a MATLAB value.
+    %
+    % This started out as a recursive descent parser, but JSON is so simple
+    % that most of the parser collapsed out.
+    %
+    % In the service of speed, simplicity, and laziness, this code is NOT a
+    % validator. Its purpose is to convert correct JSON strings to MATLAB
+    % values. It does not reject all malformed JSON.
+
+    % Copyright 2013 The MathWorks, Inc.
+
+    properties (Access = private)
+        json % the string
+        index % position in the string
+    end
+
+
+    methods (Access = private)
+
+        function this = JSON(JSONstring)
+            this.json = JSONstring;
+            this.index = 1;
+        end
+
+        function value = getValue(this)
+            % get the next value in the string
+            [token,tokenType] = this.getNextToken;
+            value = token;
+
+            if strcmp(tokenType,'Special')
+                if strcmp(token,'{')
+                    value = this.getObject;
+                elseif strcmp(token,'[')
+                    value = this.getArray;
+                end
+            end
+        end
+
+        function array = getArray(this)
+            % an array is [ value, ... ]
+            array = {};
+
+            value = this.getValue;
+            while ~strcmp(value,']')
+                % got a value
+                array{end+1} = value; %#ok<AGROW> final size is unknowable
+
+                % followed by a comma or a "]"
+                value = this.getValue;
+
+                if strcmp(value,',')
+                    value = this.getValue;
+                elseif strcmp(value,']')
+                    continue
+                else
+                    error('JSON parser requires commas between array elements');
+                end
+            end
+
+            % Arrays of all numbers are turned into numeric arrays
+            fcn = @(x) isnumeric(x) && ~isscalar(x);
+            if all(cellfun(fcn,array))
+                array = [array{:}];
+            end
+        end
+
+        function obj = getObject(this)
+            % an object is { string : value, ... }
+            obj = struct;
+            value = this.getValue;
+            while ~strcmp(value,'}')
+
+                fieldname = value;
+                % make sure its a valid structure field name
+                fieldname = strrep(fieldname,':','_');
+                fieldname = strrep(fieldname,'-','_');
+                % fix for field names that start with numbers
+                % Thanks to Guy Ziv!
+                fieldname = regexprep(fieldname,'(^\d)','s$1');
+
+                % check for colon
+                value = this.getValue;
+                if ~strcmp(value,':')
+                    error('JSON parser requires colons between object names and values');
+                end
+
+                % get the value
+                value = this.getValue;
+                obj.(fieldname) = value;
+
+                value = this.getValue;
+                if strcmp(value,',')
+                    value = this.getValue;
+                elseif strcmp(value,'}')
+                    continue
+                else
+                    error('JSON parser requires commas between object elements');
+                end
+            end
+
+        end
+
+        function [token,tokenType] = getNextToken(this)
+            % get whatever is next in the string
+
+            % skip whitespace
+            ch = this.json(this.index);
+            while isWhitespace(ch)
+                this.index = this.index + 1;
+                ch = this.json(this.index);
+            end
+
+            % is it a special character?
+            if isSpecial(ch)
+                token = ch;
+                tokenType = 'Special';
+                this.index = this.index + 1;
+                return
+            end
+
+            % is it one of the three keywords?
+            switch(ch)
+                case 't'
+                    match(this,'true');
+                    token = true;
+                    tokenType = 'Logical';
+                    return;
+                case 'f'
+                    match(this,'false');
+                    tokenType = 'Logical';
+                    token = false;
+                    return;
+                case 'n'
+                    match(this,'null');
+                    tokenType = 'Null';
+                    token = [];
+                    return;
+            end
+
+            % is it a string?
+            if(ch == '"')
+                token = getString(this);
+                tokenType = 'String';
+                return;
+            end
+
+            % well, then it better be a number
+            token = getNumber(this);
+            tokenType = 'Number';
+
+            function match(this,str)
+                % find and consume exactly str at the current location of error
+                n = length(str);
+                range = this.index:(this.index + n - 1);
+                found = this.json(range);
+                if strcmp(str,found)
+                    this.index = this.index + n;
+                else
+                    error('The JSON parser expected "%s" but found %s',str,found)
+                end
+            end
+
+            function tf = isWhitespace(aChar)
+                % space, carrage return, linefeed, horizontal tab
+                tf = aChar == 32 || aChar == 10 || aChar == 13 || aChar == 9;
+            end
+
+            function tf = isSpecial(aChar)
+                % the special characters in the JSON "language"
+                tf = aChar == '{' || aChar == '}' || aChar == '['|| aChar == ']'|| aChar == ':' || aChar == ',';
+            end
+
+            function string = getString(this)
+                first = this.index + 1;
+                last = first;
+                str = this.json;
+
+                ch = str(last);
+                while ch ~= '"'
+                    if(ch == '\\') %#ok<STCMP> We KNOW both are single chars
+                        last = last + 2;
+                    else
+                        last = last + 1;
+                    end
+                    ch = str(last);
+                end
+
+                % get the string without it's quotes
+                string = str(first:(last-1));
+                this.index = last + 1; % skip the trailing "
+            end
+
+            function number = getNumber(this)
+                first = this.index;
+                last = first;
+                ch = charAt(this,first);
+
+                if(ch == '-')
+                    last = last + 1;
+                    ch = charAt(this,last);
+                end
+
+                while isDigit(ch)
+                    last = last + 1;
+                    ch = charAt(this,last);
+                end
+
+                if(ch == '.')
+                    last = last + 1;
+                    ch = charAt(this,last);
+                    while isDigit(ch)
+                        last = last + 1;
+                        ch = charAt(this,last);
+                    end
+                end
+
+                if ch == 'e' || ch == 'E'
+                    last = last + 1;
+                    ch = charAt(this,last);
+                    if ismember(ch,'+-')
+                        last = last + 1;
+                        ch = charAt(this,last);
+                    end
+                    while isDigit(ch)
+                        last = last + 1;
+                        ch = charAt(this,last);
+                    end
+                end
+
+                % pull out the string
+                str = this.json(first:(last-1));
+                number = str2double(str);
+
+                % move past it
+                this.index = last;
+
+                % helper functions
+                function char = charAt(this,position)
+                    if(position > length(this.json))
+                        char = 0;
+                    else
+                        char = this.json(position);
+                    end
+                end
+
+                function tf = isDigit(aChar)
+                    tf = aChar > 47 && aChar < 58;
+                end
+
+            end
+
+        end
+
+    end
+
+    methods(Static)
+        % This is the one method you should call from outside the file.
+        % JSON.parse(string)... that should be familiar to Javascrpt
+        % programmers
+        function value = parse(JSONstring)
+            jsonObject = JSON(JSONstring);
+            value = jsonObject.getValue;
+        end
+    end
+
+end