separated integration tests from unit tests, updated script for slab …

…stitching

classes/@Msection/show_tile.m

@@ -57,9 +57,18 @@
         im = [];
         return;
     else
-        %[im, Wbox, imlabel] = render_poly_02(L.tiles, scale, Wbox, 0,t, mask_list, mask_fn);
-        [im, Wbox, imlabel] = render_poly_06(L.tiles, scale, Wbox, 0, stack);
+        t = obj.tiles(tile_show);
+        rc.baseURL = t.server;
+        rc.owner   = t.owner;
+        rc.project = t.project;
+        rc.stack   = t.stack;
+        im = get_image_box_renderer(rc, t.z, Wbox, scale, t.dir_temp_render, t.renderer_id);
+
 
+
+        %%% use Renderer client for getting individual tiles, and let matlab assemble them
+%         [im, Wbox, imlabel] = render_poly_06(L.tiles, scale, Wbox, 0, stack);
+%         
         warning off;imshow(im);warning on;
         %     %% optionally show the text labels overlaid onto the tile images
         if fz

external/get_image_box_renderer.m

@@ -0,0 +1,40 @@
+function [im, v] = get_image_box_renderer(rc, z, Wbox, scale, dir_temp_render, renderer_id)
+% Returns the image of a specified box in collection rc
+% use Renderer client for complete box
+%   /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/box/{x},{y},{width},{height},{scale}/jpeg-image
+%
+% Author: Khaled Khairy
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+v = [];
+fn = [dir_temp_render '/tile_image_' num2str(randi(1000)) '_' renderer_id '.jpg'];
+url = sprintf('%s/owner/%s/project/%s/stack/%s/z/%s/box/%.0f,%.0f,%.0f,%.0f,%s/render-parameters?filter=true',...
+    rc.baseURL, rc.owner, rc.project, rc.stack, num2str(z),Wbox(1), ...
+    Wbox(2), ...
+    Wbox(3), ...
+    Wbox(4), ...
+    num2str(scale));
+
+
+
+% we will try multiple times
+cmd = sprintf('/groups/flyTEM/flyTEM/render/bin/render.sh --memory 7g --out %s --parameters_url "%s"', fn, url);
+[a, resp_str] = system(cmd);
+file_ready = 0;
+count = 1;
+while ~(file_ready) && count<200
+    pause(0.05);
+    file_ready = [exist(fn,'file')==2];
+    count = count + 1;
+end
+try
+    pause(1.0);
+    im = imread(fn, 'jpeg');
+    %if nargout>1, v = webread(url);end
+catch err_reading_image
+    kk_disp_err(err_reading_image);
+    disp('Retrying');
+    pause(1.0);
+    im = imread(fn, 'jpeg');
+end
+im = rgb2gray(im);
+delete(fn);

external/get_image_box_renderer.m~

@@ -0,0 +1,39 @@
+function [im, v] = get_image_box_renderer(rc, z, Wbox, scale, dir_temp_render, renderer_id)
+% Returns the image of a specified box in collection rc
+% use Renderer client for complete box
+%   /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/box/{x},{y},{width},{height},{scale}/jpeg-image
+%
+% Author: Khaled Khairy
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+v = [];
+fn = [dir_temp_render '/tile_image_' num2str(randi(1000)) '_' renderer_id '.jpg'];
+url = sprintf('%s/owner/%s/project/%s/stack/%s/z/%s/box/%.0f,%.0f,%.0f,%.0f,%s/render-parameters?filter=true',...
+    rc.baseURL, rc.owner, rc.project, rc.stack, num2str(z),Wbox(1), ...
+    Wbox(2), ...
+    Wbox(3), ...
+    Wbox(4), ...
+    num2str(scale));
+
+if nargout>1, v = webread(url);end
+
+% we will try four times
+cmd = sprintf('/groups/flyTEM/flyTEM/render/bin/render.sh --memory 7g --out %s --parameters_url "%s"', fn, url);
+[a, resp_str] = system(cmd);
+file_ready = 0;
+count = 1;
+while ~(file_ready) && count<200
+    pause(0.01);
+    file_ready = [exist(fn,'file')==2];
+    count = count + 1;
+end
+try
+    pause(1.0);
+    im = imread(fn, 'jpeg');
+catch err_reading_image
+    kk_disp_err(err_reading_image);
+    disp('Retrying');
+    pause(1.0);
+    im = imread(fn, 'jpeg');
+end
+im = rgb2gray(im);
+delete(fn);

external/get_section_bounds_renderer.m

@@ -0,0 +1,11 @@
+function [Wbox, bbox] = get_section_bounds_renderer(rc, z)
+% returns Wbox = [x y width height] of the section L as specified in rc
+% /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/bounds 
+
+
+url = sprintf('%s/owner/%s/project/%s/stack/%s/z/%s/bounds',...
+    rc.baseURL, rc.owner, rc.project, rc.stack, num2str(z));
+
+js = webread(url);
+Wbox = [js.minX js.minY js.maxX-js.minX js.maxY-js.minY];
+bbox = [js.minX js.minY js.maxX js.maxY];

external/point_match_gen_SIFT.m

@@ -1,5 +1,5 @@
-function [m12_1, m12_2, js] = point_match_gen_SIFT(t1, t2)
-% Return point-matches based on SIFT features
+function [m12_1, m12_2, v] = point_match_gen_SIFT(url1, url2)
+% Return point-matches based on SIFT features   --- still under development
 %
 % Depends on Eric T.'s packaging of Saalfeld's code that uses SIFT and filters point matches
 % 
@@ -8,14 +8,25 @@
 %
 % Author: Khaled Khairy
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+m12_1 = [];
+m12_2 = [];
+v = [];
+if nargin<3, run_local = 1;end
+
+% URLs could be anything that the Renderer can interpret accoring to its API.
+% for example tile urls should look like this:
+% url1 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
+%                 t1.server, t1.owner, t1.project, t1.stack, t1.renderer_id);
+% url2 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
+%                 t2.server, t2.owner, t2.project, t2.stack, t2.renderer_id);
 
-% tile urls should look like this:
 %http://10.37.5.60:8080/render-ws/v1/owner/flyTEM/project/test/stack/EXP_v12_SURF_rough_1_4/tile/151215054802009008.3.0/render-parameters?filter=true
 % command issued to system
 %/groups/flyTEM/flyTEM/render/bin/gen-match.sh --memory 7G --numberOfThreads 8 --baseDataUrl "${BASE_DATA_URL}" --owner trautmane --collection test_match_gen ${TILE_URL_PAIRS} | tee -a log.txt
 
+tm = clock;
+file_code = [num2str(tm(6)) '_' num2str(randi(1000000000000))];
 
-file_code = num2str(randi(1000000)) ;
 fn_pm = ['/groups/flyTEM/home/khairyk/mwork/temp/matches_' file_code '.json'];
 fn_log = ['groups/flyTEM/home/khairyk/mwork/temp/log_' file_code '.txt'];
 
@@ -27,10 +38,6 @@
 str_collection = '--collection test_match_gen ';
 
 
-url1 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
-                t1.server, t1.owner, t1.project, t1.stack, t1.renderer_id);
-url2 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
-                t2.server, t2.owner, t2.project, t2.stack, t2.renderer_id);
 str_pairs =[url1 ' ' url2];
 
 str_parameters = [' --matchStorageFile ' fn_pm ' | tee -a ' fn_log];
@@ -39,8 +46,8 @@
 
 
 [a, resp_str] = system(str);
-disp(resp_str);
-
+%disp(resp_str);
+%wait_for_file(fn_pm, 10);
 
 %% read json file
 try
@@ -61,14 +68,14 @@
         m12_2 = m12_2(indx,:);
         m12_1 = m12_1(indx,:);
     end
-    figure; showMatchedFeatures(get_image(t1), get_image(t2), m12_1, m12_2, 'montage');
+
 else
-    warning('No point-matches found');
+    warning('No point-matches found -- empty set returned');
 end
 
 
 %% cleanup
-delete fn_pm;
+delete(fn_pm);
 
 
 

external/point_match_gen_SIFT.m~

@@ -1,5 +1,5 @@
-function [m12_1, m12_2, js] = point_match_gen_SIFT(t1, t2)
-% Return point-matches based on SIFT features
+function [m12_1, m12_2, v] = point_match_gen_SIFT(url1, url2, run_local)
+% Return point-matches based on SIFT features   --- still under development
 %
 % Depends on Eric T.'s packaging of Saalfeld's code that uses SIFT and filters point matches
 % 
@@ -8,14 +8,25 @@ function [m12_1, m12_2, js] = point_match_gen_SIFT(t1, t2)
 %
 % Author: Khaled Khairy
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+m12_1 = [];
+m12_2 = [];
+v = [];
+if nargin<3, run_local = 1;end
+
+% URLs could be anything that the Renderer can interpret accoring to its API.
+% for example tile urls should look like this:
+% url1 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
+%                 t1.server, t1.owner, t1.project, t1.stack, t1.renderer_id);
+% url2 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
+%                 t2.server, t2.owner, t2.project, t2.stack, t2.renderer_id);
 
-% tile urls should look like this:
 %http://10.37.5.60:8080/render-ws/v1/owner/flyTEM/project/test/stack/EXP_v12_SURF_rough_1_4/tile/151215054802009008.3.0/render-parameters?filter=true
 % command issued to system
 %/groups/flyTEM/flyTEM/render/bin/gen-match.sh --memory 7G --numberOfThreads 8 --baseDataUrl "${BASE_DATA_URL}" --owner trautmane --collection test_match_gen ${TILE_URL_PAIRS} | tee -a log.txt
 
+tm = clock;
+file_code = [num2str(tm(6)) '_' num2str(randi(1000000000000))];
 
-file_code = num2str(randi(1000000)) ;
 fn_pm = ['/groups/flyTEM/home/khairyk/mwork/temp/matches_' file_code '.json'];
 fn_log = ['groups/flyTEM/home/khairyk/mwork/temp/log_' file_code '.txt'];
 
@@ -27,10 +38,6 @@ str_owner = '--owner trautmane ';
 str_collection = '--collection test_match_gen ';
 
 
-url1 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
-                t1.server, t1.owner, t1.project, t1.stack, t1.renderer_id);
-url2 = sprintf('%s/owner/%s/project/%s/stack/%s/tile/%s/render-parameters?filter=true',...
-                t2.server, t2.owner, t2.project, t2.stack, t2.renderer_id);
 str_pairs =[url1 ' ' url2];
 
 str_parameters = [' --matchStorageFile ' fn_pm ' | tee -a ' fn_log];
@@ -40,7 +47,7 @@ str = [base_cmd str_memory str_n_threads str_base_data_url str_owner str_collect
 
 [a, resp_str] = system(str);
 disp(resp_str);
-
+wait_for_file(fn_pm, 10);
 
 %% read json file
 try
@@ -61,14 +68,14 @@ if ~isempty(v{1}.matches.p)
         m12_2 = m12_2(indx,:);
         m12_1 = m12_1(indx,:);
     end
-    figure; showMatchedFeatures(get_image(t1), get_image(t2), m12_1, m12_2, 'montage');
+
 else
     warning('No point-matches found');
 end
 
 
 %% cleanup
-delete fn_pm;
+delete(fn_pm);