debugs most of the API; label pushing still not working properly

README.md

@@ -60,9 +60,10 @@ Consult the application in *example* to see many of the API features exercised.
 
 ## TODO
 
-* Add test regressions
+* Add test regressions and more documentation
 * Improve performance of streaming large amounts of data by eliminating unnecessary copying.
-* Expand support to more datatype instances in DVID (like sparse volumes)
+* Expand support to more datatype instances in DVID (like sparse volumes) and handling DVID meta-data
+* Simpler package linking
 
 ## Notes
 

example/libdvid_example.cpp

@@ -6,6 +6,37 @@ using std::string;
 
 using namespace libdvid;
 
+// image 1 mask
+unsigned char img1_mask[] = {
+    0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+    0,0,1,0,0,1,0,1,1,1,1,0,1,0,0,0,0,1,0,0,0,0,0,0,1,1,0,0,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,
+    0,0,1,1,1,1,0,1,1,1,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1,
+    0,0,1,0,0,1,0,1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,
+    0,0,1,0,0,1,0,1,1,1,1,0,1,1,1,1,0,1,1,1,1,0,0,0,1,1,0,0,
+    0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
+
+// image 2 mask
+unsigned char img2_mask[] = {
+    0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,
+    0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0};
+
+int WIDTH = 28;
+int HEIGHT = 11;
+
 int main(int argc, char** argv) {
     if (argc != 3) {
         cout << "Usage: <program> <server_name> <uuid>" << endl;
@@ -20,7 +51,7 @@ int main(int argc, char** argv) {
         string label_datatype_name = "labels1";
         string keyvalue_datatype_name = "keys";
 
-        // test creation of DVID datatypes
+        // ** Test creation of DVID datatypes **
         if(!dvid_node.create_grayscale8(gray_datatype_name)) {
             cout << gray_datatype_name << " already exists" << endl;
         }
@@ -30,8 +61,61 @@ int main(int argc, char** argv) {
         if(!dvid_node.create_keyvalue(keyvalue_datatype_name)) {
             cout << keyvalue_datatype_name << " already exists" << endl;
         }
+
+        // ** Write and read grayscale data **
+        // create grayscale image volume
+        unsigned char * img_gray = new unsigned char [sizeof(img1_mask)*2];
+        for (int i = 0; i < sizeof(img1_mask); ++i) {
+            img_gray[i] = img1_mask[i] * 255;
+            img_gray[i+sizeof(img1_mask)] = img2_mask[i] * 255;
+        }
+
+        // create binary data string wrapper (no meta-data for now -- must explicitly create)
+        BinaryDataPtr graybin = BinaryData::create_binary_data((char*)(img_gray), sizeof(img1_mask)*2);
+        tuple start; start.push_back(0); start.push_back(0); start.push_back(0);
+        tuple sizes; sizes.push_back(WIDTH); sizes.push_back(HEIGHT); sizes.push_back(2);
+        tuple channels; channels.push_back(0); channels.push_back(1); channels.push_back(2);
+
+        // post grayscale volume
+        // one could also write 2D image slices but the starting location must
+        // be at least an ND point where N is greater than 2
+        dvid_node.write_volume_roi(gray_datatype_name, start, sizes, channels, graybin);
+
+        // retrieve the image volume and make sure it makes the posted volume
+        DVIDGrayPtr graycomp;
+        dvid_node.get_volume_roi(gray_datatype_name, start, sizes, channels, graycomp);
+        unsigned char* datacomp = graycomp->get_raw();
+        for (int i = 0; i < sizeof(img1_mask)*2; ++i) {
+            assert(datacomp[i] == img_gray[i]);
+        }
+
+        // ** Write and read labels64 data **
+        // create label 64 image volume
+        unsigned long long * img_labels = new unsigned long long [sizeof(img1_mask)*2];
+        for (int i = 0; i < sizeof(img1_mask); ++i) {
+            img_labels[i] = img1_mask[i] * 255;
+            img_labels[i+sizeof(img1_mask)] = img2_mask[i] * 255;
+        }
+
+        // create binary data string wrapper (64 bits per pixel)
+        BinaryDataPtr labelbin = BinaryData::create_binary_data((char*)(img_labels), sizeof(img1_mask)*2*8);
+
+        // post labels volume
+        // one could also write 2D image slices but the starting location must
+        // be at least an ND point where N is greater than 2
 
-        // test key value interface
+        // !! not currently working
+        //dvid_node.write_volume_roi(label_datatype_name, start, sizes, channels, labelbin);
+
+        // retrieve the image volume and make sure it makes the posted volume
+        DVIDLabelPtr labelcomp;
+        dvid_node.get_volume_roi(label_datatype_name, start, sizes, channels, labelcomp);
+        unsigned long long* labeldatacomp = labelcomp->get_raw();
+        for (int i = 0; i < sizeof(img1_mask)*2; ++i) {
+            //assert(labeldatacomp[i] == img_labels[i]);
+        }
+
+        // ** Test key value interface **
         Json::Value data_init;
         data_init["hello"] = "world"; 
         dvid_node.put(keyvalue_datatype_name, "spot0", data_init); 

libdvid/BinaryData.h

@@ -14,9 +14,9 @@ typedef boost::shared_ptr<BinaryData> BinaryDataPtr;
 
 class BinaryData {
   public:
-    static BinaryDataPtr create_binary_data(const char* data_)
+    static BinaryDataPtr create_binary_data(const char* data_, unsigned int length)
     {
-        return BinaryDataPtr(new BinaryData(data_));
+        return BinaryDataPtr(new BinaryData(data_, length));
     }
     static BinaryDataPtr create_binary_data(std::ifstream& fin)
     {
@@ -33,7 +33,7 @@ class BinaryData {
     }
     ~BinaryData() {}
   private:
-    BinaryData(const char* data_) : data(data_) {}
+    BinaryData(const char* data_, unsigned int length) : data(data_, length) {}
     BinaryData(std::ifstream& fin)
     {
         data.assign( (std::istreambuf_iterator<char>(fin) ),

libdvid/DVIDNode.h

@@ -23,12 +23,12 @@ class DVIDNode {
     bool create_grayscale8(std::string datatype_name);
     bool create_labels64(std::string datatype_name);
 
-    void get_gray_slice(std::string datatype_instance, tuple start,
+    void get_volume_roi(std::string datatype_instance, tuple start,
             tuple sizes, tuple channels, DVIDGrayPtr& gray);
-    void get_label_slice(std::string datatype_instance, tuple start,
+    void get_volume_roi(std::string datatype_instance, tuple start,
             tuple sizes, tuple channels, DVIDLabelPtr& labels);
 
-    void write_label_slice(std::string datatype_instance, tuple start,
+    void write_volume_roi(std::string datatype_instance, tuple start,
             tuple sizes, tuple channels, BinaryDataPtr data);
 
     // Key-Value Interface

libdvid/DVIDVoxels.h

@@ -11,11 +11,11 @@ class DVIDVoxels {
   public:
     static boost::shared_ptr<DVIDVoxels<T> > get_dvid_voxels(T* array_)
     {
-        return boost::shared_ptr<DVIDVoxels<T> >(new DVIDVoxels(array_));
+        return boost::shared_ptr<DVIDVoxels<T> >(new DVIDVoxels<T>(array_));
     }
     static boost::shared_ptr<DVIDVoxels<T> > get_dvid_voxels(std::string& data_str)
     {
-        return boost::shared_ptr<DVIDVoxels<T> >(new DVIDVoxels(data_str));
+        return boost::shared_ptr<DVIDVoxels<T> >(new DVIDVoxels<T>(data_str));
     }
 
     ~DVIDVoxels()

src/DVIDNode.cpp

@@ -10,7 +10,6 @@ using namespace boost::network;
 using std::ifstream; using std::set; using std::stringstream;
 Json::Reader json_reader;
 
-
 namespace libdvid {
 
 DVIDNode::DVIDNode(DVIDServer web_addr_, UUID uuid_) : 
@@ -65,7 +64,7 @@ void DVIDNode::put(std::string keyvalue, std::string key, Json::Value& data)
 {
     stringstream datastr;
     datastr << data;
-    BinaryDataPtr bdata = BinaryData::create_binary_data(datastr.str().c_str());
+    BinaryDataPtr bdata = BinaryData::create_binary_data(datastr.str().c_str(), datastr.str().length());
     put(keyvalue, key, bdata);
 }
 
@@ -82,7 +81,7 @@ void DVIDNode::get(std::string keyvalue, std::string key, BinaryDataPtr& value)
     }
     std::string data = body(respdata);
     // ?! allow intialization to happen in constructor
-    value = BinaryData::create_binary_data(data.c_str());
+    value = BinaryData::create_binary_data(data.c_str(), data.length());
 }
 
 void DVIDNode::get(std::string keyvalue, std::string key, Json::Value& data)
@@ -96,23 +95,23 @@ void DVIDNode::get(std::string keyvalue, std::string key, Json::Value& data)
     }
 }
 
-void DVIDNode::get_gray_slice(std::string datatype_instance, tuple start,
+void DVIDNode::get_volume_roi(std::string datatype_instance, tuple start,
         tuple sizes, tuple channels, DVIDGrayPtr& gray)
 {
     std::string volume;
     retrieve_volume(datatype_instance, start, sizes, channels, volume);
     gray = DVIDVoxels<unsigned char>::get_dvid_voxels(volume); 
 }
 
-void DVIDNode::get_label_slice(std::string datatype_instance, tuple start,
+void DVIDNode::get_volume_roi(std::string datatype_instance, tuple start,
         tuple sizes, tuple channels, DVIDLabelPtr& labels)
 {
     std::string volume;
     retrieve_volume(datatype_instance, start, sizes, channels, volume);
     labels = DVIDVoxels<unsigned long long>::get_dvid_voxels(volume); 
 }
 
-void DVIDNode::write_label_slice(std::string datatype_instance, tuple start,
+void DVIDNode::write_volume_roi(std::string datatype_instance, tuple start,
         tuple sizes, tuple channels, BinaryDataPtr data)
 {
     client::request requestobj(construct_volume_uri(

todo

@@ -1,8 +1,6 @@
--make some fake image data -- perhaps write out hello world on two planes
--debug
-
--documentation
+-documentation/fix label pushing
 
+-be careful about 0/nulls
 -find datatype_instance function
 -integration and unit tests
 -automatically include cppnet and boost libraries in build