working receptor densities and streamline counts

scalableminds · Dec 16, 2024 · 9469580 · 9469580
1 parent 27bd7a5
commit 9469580
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Showing 6 changed files with 52 additions and 73 deletions.
diff --git a/+siibra/+internal/API.m b/+siibra/+internal/API.m
@@ -5,7 +5,6 @@
         %Endpoint = "https://siibra-api-stable.apps.hbp.eu/v1_0/"
         %EndpointV2 = "https://siibra-api-stable.apps.hbp.eu/v2_0"
         EndpointV3 = "https://siibra-api-stable.apps.hbp.eu/v3_0/"
-        %EndpointV3 = "https://siibra-api-prod.apps.tc.humanbrainproject.eu/v3_0/"
     end
 
     methods (Static)
@@ -136,6 +135,31 @@
                             "&region_id=" + region.Name;
             absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink);
         end
+        function features = regionalConnectivity(parcellation, type)
+            relativeLink = "feature/RegionalConnectivity";
+            absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink);
+            parameters = ["parcellation_id=" + parcellation.Id, "type=" + type];
+            features = siibra.internal.API.collectItemsAcrossPages(absoluteLink, parameters);
+        end
+        function absoluteLink = streamlineCountsForSubject(streamlineCounts, subject)
+            relativeLink = "feature/RegionalConnectivity/" + streamlineCounts.FeatureId + ...
+                "?parcellation_id=" + streamlineCounts.Parcellation.Id + ...
+                "&type=StreamlineCounts";
+
+            if ~isempty(subject)
+                relativeLink = relativeLink + "&subject=" + subject;
+            end
+
+            absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink);
+        end
+
+        function downloadFeature(path, featureId)
+            relativeLink = "feature/" + featureId + "/download";
+            absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink);
+            siibra.internal.API.doWebsaveWithLongTimeout(path, absoluteLink);
+        end
+
+
     end
 
 end

diff --git a/+siibra/+items/+features/ReceptorDensity.m b/+siibra/+items/+features/ReceptorDensity.m
@@ -25,11 +25,10 @@
                 siibra.internal.API.tabularFeature( ...
                 obj.Region, ...
                 obj.Id));
-            fingerprintStruct = fingerprintJson.data.fingerprints;
-            receptors = fieldnames(fingerprintStruct);
-            means = arrayfun(@(i) fingerprintStruct.(receptors{i}).mean, 1:numel(receptors));
-            stds = arrayfun(@(i) fingerprintStruct.(receptors{i}).std, 1:numel(receptors));
-            fingerprints = table(means.', stds.', 'VariableNames', ["Mean", "Std"], 'RowNames', receptors);
+            data = fingerprintJson.data.data;
+            column_names = fingerprintJson.data.columns;
+            row_names = fingerprintJson.data.index;
+            fingerprints = array2table(data, 'VariableNames', column_names, 'RowNames', row_names );
         end
     end
 end

diff --git a/+siibra/+items/+features/StreamlineCounts.m b/+siibra/+items/+features/StreamlineCounts.m
@@ -6,11 +6,8 @@
         Parcellation (1, :) siibra.items.Parcellation
         Name (1, 1) string
         Cohort (1, 1) string
-        Subject (1, 1) string
-        Authors (1, :) string
+        Subjects (1, :) string
         Description (1, 1) string
-        % Citation (1, 1) string
-        Matrix uint8
         FeatureId (1, 1) string
     end
 
@@ -21,57 +18,29 @@
             obj.Parcellation = parcellation;
             obj.Name = featureJson.name;
             obj.Cohort = featureJson.cohort;
-            obj.Subject = featureJson.subject;
-            obj.Authors = featureJson.authors;
+            obj.Subjects = featureJson.subjects;
             obj.Description = featureJson.description;
-            % obj.Citation = featureJson.citation;
-            obj.FeatureId = featureJson.x_id;
+            obj.FeatureId = featureJson.id;
 
         end
-        function connectivityMatrix = get.Matrix(obj)
-            featureIdNormalized = obj.FeatureId.replace("/", "-");
-            matrixCachePath = siibra.internal.cache(featureIdNormalized + ".mat", "parcellation_features");
-            if ~isfile(matrixCachePath)
-                matrixJson = siibra.internal.API.doWebreadWithLongTimeout( ...
-                    siibra.internal.API.parcellationFeature( ...
-                    obj.Parcellation.Atlas.Id, ...
-                    obj.Parcellation.Id, ...
-                    obj.FeatureId) ...
-                    );
-                encodedMatrix = matrixJson.matrix.content;
-                dim1 = matrixJson.matrix.x_height;
-                dim2 = matrixJson.matrix.x_width;
-                decodedMatrix = matlab.net.base64decode(encodedMatrix);
-
-                % write decoded and compressed matrix to file
-                compressedMatrixCachePath = siibra.internal.cache(featureIdNormalized + ".bin.gzip", "parcellation_features");
-                f = fopen(compressedMatrixCachePath, "w");
-                fwrite(f, decodedMatrix);
-                fclose(f);
-
-                % decompress file and read it again
-                binaryMatrixCachePath = siibra.internal.cache(featureIdNormalized + ".bin", "parcellation_features");
-                gunzip(compressedMatrixCachePath, siibra.internal.cache("", "parcellation_features"));
-                f = fopen(binaryMatrixCachePath, "r");
-                decompressedMatrix = fread(f, matrixJson.matrix.dtype);
-                fclose(f);
-
-                % delete intermediate files
-                delete(compressedMatrixCachePath)
-                delete(binaryMatrixCachePath)
-
-                matrix = reshape(decompressedMatrix, dim1, dim2);
-
-                connectivityMatrix = array2table(matrix);
-                columnNameLengths = cellfun(@(n) strlength(n), matrixJson.columns);
-                columnNamesToBeTrimmed = matrixJson.columns(columnNameLengths > 63);
-                matrixJson.columns(columnNameLengths > 63) = cellfun(@(n) n(1:63), columnNamesToBeTrimmed, 'UniformOutput',false);
-                connectivityMatrix.Properties.VariableNames = matrixJson.columns;
-                connectivityMatrix.Properties.RowNames = matrixJson.columns;
-                % cache matrix
-                save(matrixCachePath, "connectivityMatrix");
-            end
-            connectivityMatrix = load(matrixCachePath, "connectivityMatrix").connectivityMatrix;
+        function connectivityMatrix = connectivityMatrixForSubject(obj, subject)
+            response = siibra.internal.API.doWebreadWithLongTimeout( ...
+                siibra.internal.API.streamlineCountsForSubject( ...
+                obj, subject ...
+                ) ...
+            );
+            matrixStruct = getfield(response.matrices, "x" + subject);
+            connectivityMatrix = array2table(matrixStruct.data, "VariableNames", {matrixStruct.columns.name}, 'RowNames', {matrixStruct.index.name});
+        end
+        function connectivityMatrix = averagedConnectivityMatrix(obj)
+            % leaving the subject field empty gives us the averaged matrix
+            response = siibra.internal.API.doWebreadWithLongTimeout( ...
+                siibra.internal.API.streamlineCountsForSubject( ...
+                obj, string.empty ...
+                ) ...
+            );
+            matrixStruct = response.matrices.x_average;
+            connectivityMatrix = array2table(matrixStruct.data, "VariableNames", {matrixStruct.columns.name}, 'RowNames', {matrixStruct.index.name});
         end
     end
 end

diff --git a/+siibra/+items/Parcellation.m b/+siibra/+items/Parcellation.m
@@ -84,22 +84,9 @@
             parentRegion = obj.RegionTree.Nodes.Region(parentId);
         end
 
-        function features = getAllFeatures(obj)
-            error("API v3 has no features on parcellation level!");
-            cached_file_name = siibra.internal.cache(obj.Name + ".mat", "parcellation_features");
-            if ~isfile(cached_file_name)
-                features = siibra.internal.API.featuresForParcellation(obj.Atlas.Id, obj.Id);
-                save(cached_file_name, 'features');
-            else
-                load(cached_file_name, 'features')
-            end
-
-        end
-
         function streamlineCounts = getStreamlineCounts(obj)
-            allFeatures = obj.getAllFeatures();
-            streamlineCountIdx = arrayfun(@(e) strcmp(e.x_type,'siibra/features/connectivity/streamlineCounts'), allFeatures);
-            streamlineCounts = arrayfun(@(json) siibra.items.features.StreamlineCounts(obj, json), allFeatures(streamlineCountIdx));
+            streamlineCountsJson = siibra.internal.API.regionalConnectivity(obj, "StreamlineCounts");
+            streamlineCounts = arrayfun(@(json) siibra.items.features.StreamlineCounts(obj, json), streamlineCountsJson);
         end
     end
 

diff --git a/step-by-step/01_atlases_and_brain_parcellations/06_spatial_properties_of_brain_regions.mlx b/step-by-step/01_atlases_and_brain_parcellations/06_spatial_properties_of_brain_regions.mlx
diff --git a/walkthrough.mlx b/walkthrough.mlx