From 9a85ef1a4d369217dea37e9b5e6b68fe8646fc0d Mon Sep 17 00:00:00 2001
From: Benoit Coste <benoit.coste@protonmail.com>
Date: Thu, 11 Feb 2021 10:08:26 +0100
Subject: [PATCH] Allow markers to have no diameters (#233)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Markers may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.

Also:
Strings in the middle of the list of points are now skipped.

ℹ️ The example file added in this commit is from C280999A-I4.asc

The following illustrates both use cases:

```lisp
( (Color Red)
  (   -0.97  -141.17    84.77)
  "<--4 boutons on a PC soma"
)  ;  End of text
```
---
 README.md                         |  2 ++
 src/readers/morphologyASC.cpp     | 26 ++++++++++++++++++--------
 tests/data/marker-with-string.asc | 12 ++++++++++++
 tests/test_2_neurolucida.py       |  5 +++++
 4 files changed, 37 insertions(+), 8 deletions(-)
 create mode 100644 tests/data/marker-with-string.asc

diff --git a/README.md b/README.md
index b25b0d2e1..9ca7f9503 100644
--- a/README.md
+++ b/README.md
@@ -573,6 +573,8 @@ The following s-expressions are parsed:
   )  ;  End of markers
   ```
 
+ℹ️ Markers can may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.
+
 ##### Usage
 
 ```python
diff --git a/src/readers/morphologyASC.cpp b/src/readers/morphologyASC.cpp
index b3f7ca0b3..04a7d72ed 100644
--- a/src/readers/morphologyASC.cpp
+++ b/src/readers/morphologyASC.cpp
@@ -76,23 +76,30 @@ class NeurolucidaParser
     }
 
   private:
-    std::tuple<Point, floatType> parse_point(NeurolucidaLexer& lex) {
+    std::tuple<Point, floatType> parse_point(NeurolucidaLexer& lex, bool is_marker) {
         lex.expect(Token::LPAREN, "Point should start in LPAREN");
-        std::array<morphio::floatType, 4> point{};  // X,Y,Z,R
-        for (auto& p : point) {
+        std::array<morphio::floatType, 4> point{};  // X,Y,Z,D
+        for (unsigned int i = 0; i < 4; i++) {
             try {
 #ifdef MORPHIO_USE_DOUBLE
-                p = std::stod(lex.consume()->str());
+                point[i] = std::stod(lex.consume()->str());
 #else
-                p = std::stof(lex.consume()->str());
+                point[i] = std::stof(lex.consume()->str());
 #endif
             } catch (const std::invalid_argument&) {
                 throw RawDataError(err_.ERROR_PARSING_POINT(lex.line_num(), lex.current()->str()));
             }
+
+            // Markers can have an s-exp (X Y Z) without diameter
+            if (is_marker && i == 2 && (lex_.peek()->str() == ")")) {
+                point[3] = 0;
+                break;
+            }
         }
 
         lex.consume();
 
+        // case where the s-exp is (X Y Z R WORD). For example: (1 1 0 1 S1)
         if (lex.current()->id == +Token::WORD) {
             lex.consume(Token::WORD);
         }
@@ -231,13 +238,14 @@ class NeurolucidaParser
             } else if (id == Token::RPAREN) {
                 return header;
             } else if (id == Token::LPAREN) {
+                const auto next_token = static_cast<Token>(peek_id);
                 if (skip_sexp(peek_id)) {
                     // skip words/strings/markers
                     lex_.consume_until_balanced_paren();
                     if (peek_id == +Token::FONT)
                         lex_.consume_until_balanced_paren();
-                } else if (is_neurite_type(static_cast<Token>(peek_id))) {
-                    header.token = static_cast<Token>(peek_id);
+                } else if (is_neurite_type(next_token)) {
+                    header.token = next_token;
                     lex_.consume();  // Advance to NeuriteType
                     lex_.consume();
                     lex_.consume(Token::RPAREN, "New Neurite should end in RPAREN");
@@ -286,7 +294,7 @@ class NeurolucidaParser
                 } else if (peek_id == +Token::NUMBER) {
                     Point point;
                     floatType radius;
-                    std::tie(point, radius) = parse_point(lex_);
+                    std::tie(point, radius) = parse_point(lex_, (header.token == Token::STRING));
                     points.push_back(point);
                     diameters.push_back(radius);
                 } else if (peek_id == +Token::LPAREN) {
@@ -300,6 +308,8 @@ class NeurolucidaParser
                     throw RawDataError(
                         err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
                 }
+            } else if (id == Token::STRING) {
+                lex_.consume();
             } else {
                 throw RawDataError(err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
             }
diff --git a/tests/data/marker-with-string.asc b/tests/data/marker-with-string.asc
new file mode 100644
index 000000000..5a2d529c7
--- /dev/null
+++ b/tests/data/marker-with-string.asc
@@ -0,0 +1,12 @@
+; The following annotation has been found in C280999A-I4.asc
+; It is a top-level annotation with a quote inside
+( (Color Red)
+  (   -0.97  -141.17    84.77)
+  "<--4 boutons on a PC soma"
+)  ;  End of text
+
+("CellBody"
+ (Color Red)
+ (CellBody)
+ (0 0 0 2)
+ )
\ No newline at end of file
diff --git a/tests/test_2_neurolucida.py b/tests/test_2_neurolucida.py
index 0e76bd346..cf8814518 100644
--- a/tests/test_2_neurolucida.py
+++ b/tests/test_2_neurolucida.py
@@ -700,3 +700,8 @@ def test_skip_imagecoord():
 def test_Sections_block():
     assert_array_equal(Morphology(DATA_DIR / 'sections-block.asc').points,
                        Morphology(DATA_DIR / 'simple.asc').points)
+
+def test_marker_with_string():
+    m = Morphology(DATA_DIR / 'marker-with-string.asc')
+    assert_array_equal(m.markers[0].points, np.array([[  -0.97    , -141.169998,   84.769997]],
+                                                     dtype=np.float32))