Devcontainer isaac and analyst (#99)

* making spawn changes and adding double handed cargo * adding devcontainer file * clean up analyst query demo; save and upload database scripts * making multiple bag loading collection creation not clash * adding multiple devcontainer profiles; load database progress * adding main for running standalone * small changes from database upload * fix lint
nasa · Jul 12, 2023 · 4c9c3ff · 4c9c3ff
1 parent e7ef39d
commit 4c9c3ff
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diff --git a/.devcontainer/analyst/Dockerfile b/.devcontainer/analyst/Dockerfile
@@ -0,0 +1,2 @@
+FROM ghcr.io/nasa/isaac_analyst_notebook
+ENV DEBIAN_FRONTEND=dialog
diff --git a/.devcontainer/analyst/devcontainer.json b/.devcontainer/analyst/devcontainer.json
@@ -0,0 +1,47 @@
+{
+	"dockerFile": "Dockerfile",
+	"build": {
+		"args": {
+			"WORKSPACE": "${containerWorkspaceFolder}"
+		}
+	},
+	"remoteUser": "root",
+	"runArgs": [
+		"--network=host",
+		"--cap-add=SYS_PTRACE",
+		"--security-opt=seccomp:unconfined",
+		"--security-opt=apparmor:unconfined",
+		"--volume=/tmp/.X11-unix:/tmp/.X11-unix"
+	],
+	"containerEnv": {
+		"DISPLAY": "${localEnv:DISPLAY}",
+		"LIBGL_ALWAYS_SOFTWARE": "1" // Needed for software rendering of opengl
+	},
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.profiles.linux": {
+			"zsh": {
+				"path": "/bin/zsh"
+			}
+		},
+		"terminal.integrated.defaultProfile.linux": "zsh"
+	},
+	"extensions": [
+		// "althack.ament-task-provider",
+		"DotJoshJohnson.xml",
+		"ms-azuretools.vscode-docker",
+		"ms-python.python",
+		"ms-vscode.cpptools",
+		"redhat.vscode-yaml",
+		"smilerobotics.urdf",
+		"streetsidesoftware.code-spell-checker",
+		"twxs.cmake",
+		"yzhang.markdown-all-in-one",
+		"zachflower.uncrustify"
+	],
+	"mounts": [
+		"source=${localWorkspaceFolder},target=/src/isaac/src,type=bind,consistency=cached",
+		"source=${localWorkspaceFolder}/../../astrobee/src,target=/src/astrobee/src,type=bind,consistency=cached"
+	],
+	"workspaceFolder": "/src/isaac/src"
+}
diff --git a/.devcontainer/isaac/Dockerfile b/.devcontainer/isaac/Dockerfile
@@ -0,0 +1,2 @@
+FROM ghcr.io/nasa/isaac_analyst_notebook
+ENV DEBIAN_FRONTEND=dialog
diff --git a/.devcontainer/isaac/devcontainer.json b/.devcontainer/isaac/devcontainer.json
@@ -0,0 +1,47 @@
+{
+	"dockerFile": "Dockerfile",
+	"build": {
+		"args": {
+			"WORKSPACE": "${containerWorkspaceFolder}"
+		}
+	},
+	"remoteUser": "root",
+	"runArgs": [
+		"--network=host",
+		"--cap-add=SYS_PTRACE",
+		"--security-opt=seccomp:unconfined",
+		"--security-opt=apparmor:unconfined",
+		"--volume=/tmp/.X11-unix:/tmp/.X11-unix"
+	],
+	"containerEnv": {
+		"DISPLAY": "${localEnv:DISPLAY}",
+		"LIBGL_ALWAYS_SOFTWARE": "1" // Needed for software rendering of opengl
+	},
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.profiles.linux": {
+			"zsh": {
+				"path": "/bin/zsh"
+			}
+		},
+		"terminal.integrated.defaultProfile.linux": "zsh"
+	},
+	"extensions": [
+		// "althack.ament-task-provider",
+		"DotJoshJohnson.xml",
+		"ms-azuretools.vscode-docker",
+		"ms-python.python",
+		"ms-vscode.cpptools",
+		"redhat.vscode-yaml",
+		"smilerobotics.urdf",
+		"streetsidesoftware.code-spell-checker",
+		"twxs.cmake",
+		"yzhang.markdown-all-in-one",
+		"zachflower.uncrustify"
+	],
+	"mounts": [
+		"source=${localWorkspaceFolder},target=/src/isaac/src,type=bind,consistency=cached",
+		"source=${localWorkspaceFolder}/../../astrobee/src,target=/src/astrobee/src,type=bind,consistency=cached"
+	],
+	"workspaceFolder": "/src/isaac/src"
+}
diff --git a/.devcontainer/remote/Dockerfile b/.devcontainer/remote/Dockerfile
@@ -0,0 +1,2 @@
+FROM ghcr.io/nasa/isaac_analyst_notebook
+ENV DEBIAN_FRONTEND=dialog
diff --git a/.devcontainer/remote/devcontainer.json b/.devcontainer/remote/devcontainer.json
@@ -0,0 +1,47 @@
+{
+	"dockerFile": "Dockerfile",
+	"build": {
+		"args": {
+			"WORKSPACE": "${containerWorkspaceFolder}"
+		}
+	},
+	"remoteUser": "root",
+	"runArgs": [
+		"--network=host",
+		"--cap-add=SYS_PTRACE",
+		"--security-opt=seccomp:unconfined",
+		"--security-opt=apparmor:unconfined",
+		"--volume=/tmp/.X11-unix:/tmp/.X11-unix"
+	],
+	"containerEnv": {
+		"DISPLAY": "${localEnv:DISPLAY}",
+		"LIBGL_ALWAYS_SOFTWARE": "1" // Needed for software rendering of opengl
+	},
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.profiles.linux": {
+			"zsh": {
+				"path": "/bin/zsh"
+			}
+		},
+		"terminal.integrated.defaultProfile.linux": "zsh"
+	},
+	"extensions": [
+		// "althack.ament-task-provider",
+		"DotJoshJohnson.xml",
+		"ms-azuretools.vscode-docker",
+		"ms-python.python",
+		"ms-vscode.cpptools",
+		"redhat.vscode-yaml",
+		"smilerobotics.urdf",
+		"streetsidesoftware.code-spell-checker",
+		"twxs.cmake",
+		"yzhang.markdown-all-in-one",
+		"zachflower.uncrustify"
+	],
+	"mounts": [
+		"source=${localWorkspaceFolder},target=/src/isaac/src,type=bind,consistency=cached",
+		"source=${localWorkspaceFolder}/../../astrobee/src,target=/src/astrobee/src,type=bind,consistency=cached"
+	],
+	"workspaceFolder": "/src/isaac/src"
+}
diff --git a/.gitignore b/.gitignore
@@ -58,7 +58,9 @@ analyst/workspace/.ipython
 analyst/workspace/.jupyter
 analyst/workspace/.local
 analyst/workspace/.ipynb_checkpoints
+analyst/workspace/scripts/.ipynb_checkpoints
 analyst/workspace/.cache
+analyst/workspace/data
 
 # vscode
 isaac.code-workspace
diff --git a/analyst/tools/query_view_points.cc b/analyst/tools/query_view_points.cc
@@ -51,6 +51,27 @@ DEFINE_string(camera, "sci_cam", "Camera name.");
 DEFINE_double(min_distance,         0.2, "Anomaly: minimum distance to target (m)");
 DEFINE_double(max_distance,         0.7, "Anomaly: maximum distance to target (m)");
 
+Eigen::Vector3d read_vector(Json::Value element) {
+  Eigen::Vector3d vector_out;
+  vector_out[0] = element[0].asFloat();
+  vector_out[1] = element[1].asFloat();
+  vector_out[2] = element[2].asFloat();
+  return vector_out;
+}
+
+Eigen::Vector2d rescale_image(Eigen::Vector2d cam_size, int x, int y, int width, int height) {
+  Eigen::Vector2d vector_out;
+  vector_out[0] = x * width  / cam_size[0];
+  vector_out[1] = y * height / cam_size[1];
+  return vector_out;
+}
+Json::Value vector_2d_to_json(Eigen::Vector2d coord) {
+  Json::Value coord_json;
+  coord_json[0] = coord[0];
+  coord_json[1] = coord[1];
+  return coord_json;
+}
+
 int main(int argc, char** argv) {
   // Gather some data from the command
   google::SetUsageMessage("Usage: rosrun inspection query_view_points <opts>");
@@ -96,9 +117,6 @@ int main(int argc, char** argv) {
   inspection::CameraView camera(cam_params, 2.0, 0.19, msg_pointer);
 
 
-
-
-
   // Extract the input list from the command-line argument
   std::string input_json = argv[1];
 
@@ -113,54 +131,72 @@ int main(int argc, char** argv) {
       std::cerr << "Input JSON does not represent an array." << std::endl;
       return 1;
   }
-  std::stringstream output_json;
+  Json::Value output_json;
   // Process each list element
   for (const auto& element : json) {
     // Assuming each list element has two dictionaries
-    if (element.size() != 2 || !element[0].isObject() || !element[1].isArray()) {
-      std::cerr << "Invalid list element encountered." << std::endl;
+    if (element.size() != 13) {
+      std::cerr << "Invalid list element encountered. Haz size " << element.size() << std::endl;
       continue;
     }
 
-    // // Extract values from the first dictionary
-    // const Json::Value& dict1 = element[0];
-    // // Access the values using the desired keys
-    // int seq = dict1["seq"].asInt();
-    // int secs = dict1["stamp"]["secs"].asInt();
-    // int nsecs = dict1["stamp"]["nsecs"].asInt();
-    // std::string frame_id = dict1["frame_id"].asString();
-
-    // Extract values from the second dictionary (assuming it contains 7 float values)
-    const Json::Value& dict = element[1];
-    std::vector<float> floatValues;
-    for (const auto& value : dict) {
-      if (value.isConvertibleTo(Json::realValue))
-        floatValues.push_back(value.asFloat());
-    }
-
-    Eigen::Vector3d target;
-    target[0] = element[1][0].asFloat();
-    target[1] = element[1][1].asFloat();
-    target[2] = element[1][2].asFloat();
     geometry_msgs::Pose ground_truth;
-    ground_truth.position.x = element[1][3].asFloat();
-    ground_truth.position.y = element[1][4].asFloat();
-    ground_truth.position.z = element[1][5].asFloat();
-    ground_truth.orientation.x = element[1][6].asFloat();
-    ground_truth.orientation.y = element[1][7].asFloat();
-    ground_truth.orientation.z = element[1][8].asFloat();
-    ground_truth.orientation.w = element[1][9].asFloat();
+    ground_truth.position.x = element[1].asFloat();
+    ground_truth.position.y = element[2].asFloat();
+    ground_truth.position.z = element[3].asFloat();
+    ground_truth.orientation.x = element[4].asFloat();
+    ground_truth.orientation.y = element[5].asFloat();
+    ground_truth.orientation.z = element[6].asFloat();
+    ground_truth.orientation.w = element[7].asFloat();
+    Eigen::Vector3d target = read_vector(element[8]);
+    Eigen::Vector3d c1 = read_vector(element[9]);
+    Eigen::Vector3d c2 = read_vector(element[10]);
+    Eigen::Vector3d c3 = read_vector(element[11]);
+    Eigen::Vector3d c4 = read_vector(element[12]);
 
     int x, y;
-
-    if (camera.GetCamXYFromPoint((msg_conversions::ros_pose_to_eigen_transform(ground_truth) *
-    transform_body_to_cam).inverse(), target, x, y)) {
-    output_json << element;
+    int height = 4008;
+    int width = 5344;
+    int c1_x, c1_y, c2_x, c2_y, c3_x, c3_y, c4_x, c4_y;
+    if (camera.GetCamXYFromPoint(msg_conversions::ros_pose_to_eigen_transform(ground_truth), target, x, y)) {
+      Json::Value output_element_json;
+      output_element_json["img"] = element[0];
+
+      Eigen::Vector2d cam_size = (cam_params.GetDistortedSize()).cast<double>();
+
+      Eigen::Vector2d coord = rescale_image(cam_size, x, y, width, height);
+      output_element_json["coord"] = vector_2d_to_json(coord);
+
+      if (!camera.GetCamXYFromPoint(msg_conversions::ros_pose_to_eigen_transform(ground_truth), c1, c1_x, c1_y)) {
+        continue;
+      }
+      Eigen::Vector2d coord_c1 = rescale_image(cam_size, c1_x, c1_y, width, height);
+      output_element_json["coord_c1"] = vector_2d_to_json(coord_c1);
+
+      if (!camera.GetCamXYFromPoint(msg_conversions::ros_pose_to_eigen_transform(ground_truth), c2, c2_x, c2_y)) {
+        continue;
+      }
+      Eigen::Vector2d coord_c2 = rescale_image(cam_size, c2_x, c2_y, width, height);
+      output_element_json["coord_c2"] = vector_2d_to_json(coord_c2);
+
+      if (!camera.GetCamXYFromPoint(msg_conversions::ros_pose_to_eigen_transform(ground_truth), c3, c3_x, c3_y)) {
+        continue;
+      }
+      Eigen::Vector2d coord_c3 = rescale_image(cam_size, c3_x, c3_y, width, height);
+      output_element_json["coord_c3"] = vector_2d_to_json(coord_c3);
+
+      if (!camera.GetCamXYFromPoint(msg_conversions::ros_pose_to_eigen_transform(ground_truth), c4, c4_x, c4_y)) {
+        continue;
+      }
+      Eigen::Vector2d coord_c4 = rescale_image(cam_size, c4_x, c4_y, width, height);
+      output_element_json["coord_c4"] = vector_2d_to_json(coord_c4);
+
+      output_json.append(output_element_json);
     }
   }
 
   // Print the output JSON
-  std::cout << output_json.str() << std::endl;
+  std::cout << output_json << std::endl;
 
   // Finish commandline flags
   google::ShutDownCommandLineFlags();

diff --git a/analyst/workspace/1_import_bagfiles.ipynb b/analyst/workspace/1_import_bagfiles.ipynb
@@ -10,38 +10,7 @@
     "\n",
     "The database used is ArangoDB. If you followed the Analyst notebook startup procedure [here](https://nasa.github.io/isaac/html/index.html), the local database should already be hosted in http://localhost:8529.\n",
     "\n",
-    "Go ahead open the link at take a look! The username is `root` and the password `isaac`.\n",
-    "\n",
-    "To connect to the database:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Connected to database!\n"
-     ]
-    }
-   ],
-   "source": [
-    "from pyArango.connection import *\n",
-    "\n",
-    "# Connect to the database\n",
-    "conn = Connection(arangoURL=\"http://iui_arangodb:8529\", username=\"root\", password=\"isaac\")\n",
-    "\n",
-    "# Open the isaac database / create it if it does not exist\n",
-    "if not conn.hasDatabase(\"isaac\"):\n",
-    "    conn.createDatabase(name=\"isaac\")\n",
-    "    \n",
-    "db = conn[\"isaac\"]    \n",
-    "print(\"Connected to database!\")"
+    "Go ahead open the link at take a look! The username is `root` and the password `isaac`."
    ]
   },
   {