From 42058f55f7c4060bb1a2f716d2bbb006fa52a9a3 Mon Sep 17 00:00:00 2001
From: Pramod Kumbhar <pramod.kumbhar@epfl.ch>
Date: Tue, 7 May 2019 18:59:47 +0200
Subject: [PATCH] Added AST visualization functionality based on d3 (#178)

  - nmodl.ast now has ast_view function that visualize in memory AST
    representation using d3.js based radial tree
  - necessary html, css and js files are added
  - get_nmodl_example_dir is removed and taken case by python modules

Todo: utility tools should be outside the main repo (see #190)
---
 CMakeLists.txt            |   2 +
 nmodl/ast.py              |  32 +++++
 nmodl/config.py.in        |   2 +
 nmodl/dsl.py              |  12 ++
 share/viz/css/tree.css    |  51 +++++++
 share/viz/index.html      |  18 +++
 share/viz/js/d3.min.js    |   5 +
 share/viz/js/tree.js      | 289 ++++++++++++++++++++++++++++++++++++++
 src/config/config.cpp.in  |   4 -
 src/config/config.h       |  18 ---
 src/pybind/CMakeLists.txt |   4 +-
 src/pybind/pynmodl.cpp    |   8 --
 12 files changed, 413 insertions(+), 32 deletions(-)
 create mode 100644 nmodl/config.py.in
 create mode 100644 share/viz/css/tree.css
 create mode 100644 share/viz/index.html
 create mode 100644 share/viz/js/d3.min.js
 create mode 100644 share/viz/js/tree.js

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4e98f9e9a4..54e1742787 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -110,6 +110,8 @@ set(PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR})
 # generate file with version number from git and nrnunits.lib file path
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/src/config/config.cpp.in
                ${CMAKE_CURRENT_BINARY_DIR}/config.cpp @ONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nmodl/config.py.in ${PROJECT_SOURCE_DIR}/nmodl/config.py
+               @ONLY)
 
 # generate Doxyfile with correct source paths
 configure_file(${PROJECT_SOURCE_DIR}/docs/Doxyfile.in ${PROJECT_SOURCE_DIR}/docs/Doxyfile)
diff --git a/nmodl/ast.py b/nmodl/ast.py
index 2002bd825f..811ad9675c 100644
--- a/nmodl/ast.py
+++ b/nmodl/ast.py
@@ -1 +1,33 @@
 from ._nmodl.ast import *  # noqa
+from .config import *
+
+def ast_view(nmodl_ast):
+    """Visualize given NMODL AST by converting to JSON form"""
+    from ._nmodl import to_json
+    from distutils.dir_util import copy_tree
+    import getpass
+    import json
+    import os
+    import tempfile
+    import webbrowser
+
+    installed_viz_tool = os.path.join(PROJECT_INSTALL_DIR, "share", "viz")
+    if os.path.exists(installed_viz_tool):
+        viz_tool_dir = installed_viz_tool
+    else:
+        viz_tool_dir = os.path.join(PROJECT_SOURCE_DIR, "share", "viz")
+
+    work_dir = os.path.join(tempfile.gettempdir(), getpass.getuser(), "nmodl")
+
+    # first copy necessary files to temp work directory
+    copy_tree(viz_tool_dir, work_dir)
+
+    # prepare json data
+    with open(os.path.join(work_dir, 'ast.js'), 'w') as outfile:
+        json_data = json.loads(to_json(nmodl_ast, True, True, True))
+        outfile.write('var astRoot = %s;' % json.dumps(json_data))
+
+    # open browser with ast
+    url = 'file://' + os.path.join(work_dir, "index.html")
+    webbrowser.open(url, new=1, autoraise=True)
+
diff --git a/nmodl/config.py.in b/nmodl/config.py.in
new file mode 100644
index 0000000000..271d07d06c
--- /dev/null
+++ b/nmodl/config.py.in
@@ -0,0 +1,2 @@
+PROJECT_SOURCE_DIR="@PROJECT_SOURCE_DIR@"
+PROJECT_INSTALL_DIR="@CMAKE_INSTALL_PREFIX@"
diff --git a/nmodl/dsl.py b/nmodl/dsl.py
index e99f2af1d0..3e0414e612 100644
--- a/nmodl/dsl.py
+++ b/nmodl/dsl.py
@@ -1 +1,13 @@
 from ._nmodl import *
+from .config import *
+
+
+def example_dir():
+    import os
+    """Return directory containing NMODL examples"""
+    installed_example = os.path.join(PROJECT_INSTALL_DIR, "share", "example")
+    if os.path.exists(installed_example):
+        return installed_example
+    else:
+        return os.path.join(PROJECT_SOURCE_DIR, "share", "example")
+
diff --git a/share/viz/css/tree.css b/share/viz/css/tree.css
new file mode 100644
index 0000000000..272ef1db6b
--- /dev/null
+++ b/share/viz/css/tree.css
@@ -0,0 +1,51 @@
+#ast {
+    position: fixed;
+    left: 0px;
+    right: 0px;
+    top: 0px;
+    bottom: 0px;
+}
+
+.node {
+    cursor: pointer;
+}
+
+.node circle {
+    fill: #ffc8c8 !important;
+    stroke: #c57bc4;
+    stroke-width: 2.5px;
+}
+
+.node text {
+    font-size: 12px !important;
+    font-family: sans-serif;
+    fill: #1f1f92;
+}
+
+.link {
+    fill: none;
+    stroke: #DCA5DB;
+    stroke-width: 3px;
+}
+
+.templink {
+    fill: none;
+    stroke: red;
+    stroke-width: 3px;
+}
+
+.dots {
+    cursor: pointer;
+}
+
+.tooltip {
+    background: #23298aeb;
+    white-space: pre;
+    padding: 10px;
+    border-radius: 3px;
+    color: white;
+    font-size: 13px;
+    font-family: "Monaco";
+    position: "absolute";
+    z-index: 10;
+}
diff --git a/share/viz/index.html b/share/viz/index.html
new file mode 100644
index 0000000000..0ce10d41fb
--- /dev/null
+++ b/share/viz/index.html
@@ -0,0 +1,18 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <meta charset="UTF-8">
+    <title>NMODL AST Visualization</title>
+    <link rel="stylesheet" href="css/tree.css">
+</head>
+
+<body>
+    <div id="ast"></div>
+
+    <script src="js/d3.min.js"></script>
+    <script src="ast.js"></script>
+    <script src="js/tree.js"></script>
+</body>
+
+</html>
diff --git a/share/viz/js/d3.min.js b/share/viz/js/d3.min.js
new file mode 100644
index 0000000000..34d5513ebf
--- /dev/null
+++ b/share/viz/js/d3.min.js
@@ -0,0 +1,5 @@
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\ No newline at end of file
diff --git a/share/viz/js/tree.js b/share/viz/js/tree.js
new file mode 100644
index 0000000000..dbca057bc8
--- /dev/null
+++ b/share/viz/js/tree.js
@@ -0,0 +1,289 @@
+// main container
+var astDiv = document.getElementById("ast");
+
+// by default show 0 to 2 depth
+var collapseDepth = 2;
+
+/// redraw AST when browser window resizes
+function redrawAST() {
+    /// get container and compute visible size
+    var astDiv = document.getElementById("ast");
+    var width = astDiv.clientWidth;
+    var height = astDiv.clientHeight;
+
+    /// ast diameter is shortest of width and height
+    var diameter = width < height ? width : height;
+
+    // define layout for tree
+    var tree = d3.layout.tree()
+        .size([360, diameter / 2 - 80])
+        .separation(function(a, b) {
+            return (a.parent == b.parent ? 7 : 10) / a.depth;
+        });
+
+    /// angle for arcs
+    var diagonal = d3.svg.diagonal.radial()
+        .projection(function(d) {
+            return [d.y, d.x / 180 * Math.PI];
+        });
+
+    /// d3 tree should start at the centre of browser
+    var centerX = width / 2;
+    var centerY = height / 2;
+
+    // any previous svg container and tooltip show be removed
+    d3.select("svg").remove();
+    d3.select("div.tooltip").remove();
+
+    /// select ast svg
+    var astSvg = d3.select(astDiv).append("svg")
+        .attr("width", width)
+        .attr("height", height)
+        .append("g")
+        .attr("class","treearea")
+        .attr("transform", "translate(" + centerX + "," + centerY + ")");
+
+    /// add div for tooltop
+    var tooltip = d3.select("body")
+        .append("div")
+        .attr('class', 'tooltip')
+        .style("position", "absolute")
+        .style("z-index", "10")
+        .style("opacity", 0)
+        .style('pointer-events', 'none')
+
+	/// set position for tree
+    astRoot.x0 = height / 2;
+    astRoot.y0 = 0;
+
+    /// first need to draw then collaprse to necessary depth and then redraw
+    drawTree(astRoot, astSvg, astRoot);
+    collapseToDepth(astRoot, collapseDepth);
+    drawTree(astRoot, astSvg, astRoot);
+
+    /// draw main ast
+    function drawTree(source, destnode, astRoot) {
+        /// counter for ids
+        var idCounter = 0;
+
+        /// animation duration
+        var duration = 200;
+
+        /// compute the new tree layout
+        var nodes = tree.nodes(astRoot),
+            links = tree.links(nodes);
+
+        /// normalize for fixed-depth
+        nodes.forEach(function(d) {
+            d.y = d.depth * 100;
+        });
+
+        /// update the nodes
+        var node = destnode.selectAll("g.node")
+            .data(nodes, function(d) {
+                return d.id || (d.id = ++idCounter);
+            });
+
+        /// enter any new nodes at the parent's previous position
+        var nodeEnter = node.enter().append("g")
+            .attr("class", "node");
+
+        /// draw little circle for each node with mouse events
+        nodeEnter.append("circle")
+            .attr("r", 1e-6)
+            .style("fill", function(d) {
+                return d._children ? "lightsteelblue" : "#fff";
+            }).on("mouseover", function(d) {
+                mouseover(d);
+            })
+            .on("mousemove", function(d) {
+                mousemove(d)
+            })
+            .on("mouseout", function() {
+                mouseout();
+            })
+            .on("click", function(d) {
+                click(d, destnode, astRoot);
+            });
+
+        /// add ast node type as title
+        nodeEnter.append("text")
+            .attr("x", 10)
+            .attr("dy", ".95em")
+            .attr("text-anchor", "start")
+            .text(function(d) {
+                return d.name;
+            })
+            .style("fill-opacity", 1e-6);
+
+
+        // transformations nodes to their new position
+
+        var nodeUpdate = node.transition()
+            .duration(duration)
+            .attr("transform", function(d) {
+                return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")";
+            })
+
+        nodeUpdate.select("circle")
+            .attr("r", 6.0)
+            .style("fill", function(d) {
+                return d._children ? "lightsteelblue" : "#fff";
+            });
+
+        nodeUpdate.select("text")
+            .style("fill-opacity", 1)
+            .attr("transform", function(d) {
+                return d.x < 180 ? "translate(0)" : "rotate(180)translate(-" + (d.name.length + 50) + ")";
+            });
+
+
+        /// transformations when nodes are made hidden
+
+        var nodeExit = node.exit().transition()
+            .duration(duration)
+            .remove();
+
+        nodeExit.select("circle")
+            .attr("r", 1e-6);
+
+        nodeExit.select("text")
+            .style("fill-opacity", 1e-6);
+
+        /// update the link
+        var link = destnode.selectAll("path.link")
+            .data(links, function(d) {
+                return d.target.id;
+            });
+
+        /// enter any new links at the parent's previous position
+        link.enter().insert("path", "g")
+            .attr("class", "link")
+            .attr("d", function(d) {
+                var o = {
+                    x: source.x0,
+                    y: source.y0
+                };
+                return diagonal({
+                    source: o,
+                    target: o
+                });
+            });
+
+        /// transition links to their new position
+        link.transition()
+            .duration(duration)
+            .attr("d", diagonal);
+
+        /// transition exiting nodes to the parent's new position
+        link.exit().transition()
+            .duration(duration)
+            .attr("d", function(d) {
+                var o = {
+                    x: source.x,
+                    y: source.y
+                };
+                return diagonal({
+                    source: o,
+                    target: o
+                });
+            })
+            .remove();
+
+        /// stash the old positions for transition
+        nodes.forEach(function(d) {
+            d.x0 = d.x;
+            d.y0 = d.y;
+        });
+
+        /// setup zoom listener
+        d3.select("svg")
+            .call(d3.behavior.zoom().scaleExtent([0.2, 5]).on("zoom", zoom));
+    }
+
+    /// make tooltip visible
+    function mouseover(d) {
+        if (d.nmodl) {
+            tooltip.text(d.nmodl);
+        } else {
+            tooltip.text(d.name);
+        }
+        d3.select('div.tooltip').
+            transition()
+            .delay(100)
+            .duration(300)
+            .style("opacity", 100)
+            .style('pointer-events', 'none')
+        return tooltip;
+    }
+
+    /// move tooltip with text as move moves
+    function mousemove(d) {
+        var height = Math.round(Number(tooltip.style('height').slice(0, -2)));
+        var top = (d3.event.pageY - (height / 2.0)) + "px";
+        var left = (d3.event.pageX + 15) + "px";
+        return tooltip.style("top", top).style("left", left);
+    }
+
+    /// hide tooltip if mouse goes out
+    function mouseout() {
+        d3.select('div.tooltip').
+            transition()
+            .delay(100)
+            .duration(300)
+            .style("opacity", 0)
+            .style('pointer-events', 'none');
+        return tooltip;
+    }
+
+    /// toggle children on click
+    function click(d, destnode, astRoot) {
+        if (d.children) {
+            d._children = d.children;
+            d.children = null;
+        } else {
+            d.children = d._children;
+            d._children = null;
+        }
+        drawTree(d, destnode, astRoot);
+    }
+
+    /// collapse nodes
+    function collapse(d) {
+        if (d.children) {
+            d._children = d.children;
+            d._children.forEach(collapse);
+            d.children = null;
+        }
+    }
+
+    /// collaprse ast to given depth
+    function collapseToDepth(node, depth) {
+        if (node.depth > depth) {
+            collapse(node);
+        }
+        if (node.depth <= depth) {
+            node.children = node.children || node._children;
+        }
+        if (!node.children) {
+            return;
+        }
+        node.children.forEach(function(n) {
+            collapseToDepth(n, depth);
+        });
+    }
+
+    /// zoom-in/out ast drawing area
+    function zoom() {
+        var scale = d3.event.scale;
+        d3.select(".treearea")
+          .attr("transform", "translate(" + centerX + "," + centerY + ") scale(" + scale + ")");
+    }
+}
+
+
+/// draw for the first time
+redrawAST();
+
+/// Redraw based on the new size whenever the browser window is resized
+window.addEventListener("resize", redrawAST);
diff --git a/src/config/config.cpp.in b/src/config/config.cpp.in
index 520169d4cb..c6158e1ddd 100644
--- a/src/config/config.cpp.in
+++ b/src/config/config.cpp.in
@@ -22,7 +22,3 @@ const std::string nmodl::Version::NMODL_VERSION = "@PROJECT_VERSION@";
  */
 const std::vector<std::string> nmodl::NrnUnitsLib::NRNUNITSLIB_PATH =
     {"@CMAKE_INSTALL_PREFIX@/share/nrnunits.lib", "@PROJECT_SOURCE_DIR@/share/nrnunits.lib"};
-
- /// Path of nmodl examples
-const std::vector<std::string> nmodl::Config::NMODL_EXAMPLE_PATH =
-        {"@CMAKE_INSTALL_PREFIX@/share/example", "@PROJECT_SOURCE_DIR@/share/example"};
\ No newline at end of file
diff --git a/src/config/config.h b/src/config/config.h
index 6934550fd0..486f70e03f 100644
--- a/src/config/config.h
+++ b/src/config/config.h
@@ -60,22 +60,4 @@ struct NrnUnitsLib {
     }
 };
 
-/**
- * \brief Information about NMODL configurations (from share directory)
- */
-struct Config {
-    /// directories with nmodl examples
-    static const std::vector<std::string> NMODL_EXAMPLE_PATH;
-
-    /// Return path nmodl example directory
-    static std::string get_nmodl_example_dir() {
-        for (const auto& path: NMODL_EXAMPLE_PATH) {
-            if (nmodl::utils::is_dir_exist(path)) {
-                return path;
-            }
-        }
-        throw std::runtime_error("Could not found nmodl example directory");
-    }
-};
-
 }  // namespace nmodl
diff --git a/src/pybind/CMakeLists.txt b/src/pybind/CMakeLists.txt
index a31f1b1d1f..90495cb2e8 100644
--- a/src/pybind/CMakeLists.txt
+++ b/src/pybind/CMakeLists.txt
@@ -3,7 +3,7 @@
 # =============================================================================
 set_source_files_properties(${AUTO_GENERATED_FILES} PROPERTIES GENERATED TRUE)
 
-foreach(file ode.py dsl.py __init__.py)
+foreach(file ast.py config.py dsl.py ode.py symtab.py visitor.py __init__.py)
   list(APPEND NMODL_PYTHON_FILES_IN ${PROJECT_SOURCE_DIR}/nmodl/${file})
   list(APPEND NMODL_PYTHON_FILES_OUT ${PROJECT_BINARY_DIR}/nmodl/${file})
 endforeach()
@@ -48,4 +48,4 @@ add_custom_command(OUTPUT ${NMODL_PYTHON_FILES_OUT}
 # Install python binding components
 # =============================================================================
 install(TARGETS _nmodl DESTINATION lib/python/nmodl)
-install(DIRECTORY ${PROJECT_SOURCE_DIR}/nmodl DESTINATION lib/python/ FILES_MATCHING PATTERN "*.py")
+install(DIRECTORY ${CMAKE_BINARY_DIR}/nmodl DESTINATION lib/python/ FILES_MATCHING PATTERN "*.py")
diff --git a/src/pybind/pynmodl.cpp b/src/pybind/pynmodl.cpp
index 4a48d7dcf4..7bda1dbb16 100644
--- a/src/pybind/pynmodl.cpp
+++ b/src/pybind/pynmodl.cpp
@@ -36,10 +36,6 @@ namespace nmodl {
 /** \brief docstring of Python exposed API */
 namespace docstring {
 
-static const char* get_nmodl_example_dir = R"(
-    Get directory with NMODL examples
-)";
-
 static const char* driver = R"(
     This is the NmodlDriver class documentation
 )";
@@ -148,10 +144,6 @@ PYBIND11_MODULE(_nmodl, m_nmodl) {
     m_nmodl.doc() = "NMODL : Source-to-Source Code Generation Framework";
     m_nmodl.attr("__version__") = nmodl::Version::NMODL_VERSION;
 
-    m_nmodl.def("example_dir",
-                &nmodl::Config::get_nmodl_example_dir,
-                nmodl::docstring::get_nmodl_example_dir);
-
     py::class_<nmodl::PyNmodlDriver> nmodl_driver(m_nmodl, "NmodlDriver", nmodl::docstring::driver);
     nmodl_driver.def(py::init<>())
         .def("parse_string",