morphio 2.6.0__tar.gz → 2.6.2__tar.gz

{MorphIO-2.6.0 → MorphIO-2.6.2}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.0
+Version: 2.6.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -356,7 +356,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
         https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
         
@@ -501,7 +501,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
         
         ```lisp
@@ -535,17 +535,40 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
             (9 10 11 6)
             )
             ```
-        - An sexp with one of the following top level s-exp:
-          * Dot
-          * FilledCircle
-          * SnowFlake
-          * Asterisk
-          * OpenCircle
-          * OpenStar
-          * Flower
-          * OpenSquare
-          * FilledStar
-          * DoubleCircle
+        - An sexp with one of the following top level regular expression:
+        
+          - Dot[0-9]*
+          - Plus[0-9]*
+          - Cross[0-9]*
+          - Splat[0-9]*
+          - Flower[0-9]*
+          - Circle[0-9]*
+          - Flower[0-9]*
+          - TriStar[0-9]*
+          - OpenStar[0-9]*
+          - Asterisk[0-9]*
+          - SnowFlake[0-9]*
+          - OpenCircle[0-9]*
+          - ShadedStar[0-9]*
+          - FilledStar[0-9]*
+          - TexacoStar[0-9]*
+          - MoneyGreen[0-9]*
+          - DarkYellow[0-9]*
+          - OpenSquare[0-9]*
+          - OpenDiamond[0-9]*
+          - CircleArrow[0-9]*
+          - CircleCross[0-9]*
+          - OpenQuadStar[0-9]*
+          - DoubleCircle[0-9]*
+          - FilledSquare[0-9]*
+          - MalteseCross[0-9]*
+          - FilledCircle[0-9]*
+          - FilledDiamond[0-9]*
+          - FilledQuadStar[0-9]*
+          - OpenUpTriangle[0-9]*
+          - FilledUpTriangle[0-9]*
+          - OpenDownTriangle[0-9]*
+          - FilledDownTriangle[0-9]*
         
           Example:
           ```lisp
@@ -557,6 +580,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
           )  ;  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
@@ -578,6 +603,26 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         assert_array_equal(pia.diameters, [3, 4, 5, 6])
         ```
         
+        ⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+        
+        ```python
+        ( (Color White)  ; [10,1]
+          (Dendrite)
+          ( -290.87  -113.09   -16.32     2.06)  ; Root
+          ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+          (
+            ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+            ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+            (Cross  ;  [3,3]
+              (Color Orange)
+              (Name "Marker 3")
+              ( -271.87  -121.14   -16.27     0.69)  ; 1
+              ( -269.34  -122.29   -15.48     0.69)  ; 2
+            )  ;  End of markers
+          )
+         )
+        ```
+        
         </details>
         
         ### Tips

{MorphIO-2.6.0 → MorphIO-2.6.2}/MorphIO.egg-info/SOURCES.txt

@@ -137,6 +137,7 @@ tests/data/circle_contour.asc
 tests/data/complexe.swc
 tests/data/disconnected_neurite.swc
 tests/data/iterators.asc
+tests/data/marker-with-string.asc
 tests/data/mono-type.asc
 tests/data/multiple_point_section.asc
 tests/data/multiple_soma.swc

{MorphIO-2.6.0 → MorphIO-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.0
+Version: 2.6.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -356,7 +356,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
         https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
         
@@ -501,7 +501,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
         
         ```lisp
@@ -535,17 +535,40 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
             (9 10 11 6)
             )
             ```
-        - An sexp with one of the following top level s-exp:
-          * Dot
-          * FilledCircle
-          * SnowFlake
-          * Asterisk
-          * OpenCircle
-          * OpenStar
-          * Flower
-          * OpenSquare
-          * FilledStar
-          * DoubleCircle
+        - An sexp with one of the following top level regular expression:
+        
+          - Dot[0-9]*
+          - Plus[0-9]*
+          - Cross[0-9]*
+          - Splat[0-9]*
+          - Flower[0-9]*
+          - Circle[0-9]*
+          - Flower[0-9]*
+          - TriStar[0-9]*
+          - OpenStar[0-9]*
+          - Asterisk[0-9]*
+          - SnowFlake[0-9]*
+          - OpenCircle[0-9]*
+          - ShadedStar[0-9]*
+          - FilledStar[0-9]*
+          - TexacoStar[0-9]*
+          - MoneyGreen[0-9]*
+          - DarkYellow[0-9]*
+          - OpenSquare[0-9]*
+          - OpenDiamond[0-9]*
+          - CircleArrow[0-9]*
+          - CircleCross[0-9]*
+          - OpenQuadStar[0-9]*
+          - DoubleCircle[0-9]*
+          - FilledSquare[0-9]*
+          - MalteseCross[0-9]*
+          - FilledCircle[0-9]*
+          - FilledDiamond[0-9]*
+          - FilledQuadStar[0-9]*
+          - OpenUpTriangle[0-9]*
+          - FilledUpTriangle[0-9]*
+          - OpenDownTriangle[0-9]*
+          - FilledDownTriangle[0-9]*
         
           Example:
           ```lisp
@@ -557,6 +580,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
           )  ;  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
@@ -578,6 +603,26 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         assert_array_equal(pia.diameters, [3, 4, 5, 6])
         ```
         
+        ⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+        
+        ```python
+        ( (Color White)  ; [10,1]
+          (Dendrite)
+          ( -290.87  -113.09   -16.32     2.06)  ; Root
+          ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+          (
+            ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+            ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+            (Cross  ;  [3,3]
+              (Color Orange)
+              (Name "Marker 3")
+              ( -271.87  -121.14   -16.27     0.69)  ; 1
+              ( -269.34  -122.29   -15.48     0.69)  ; 2
+            )  ;  End of markers
+          )
+         )
+        ```
+        
         </details>
         
         ### Tips

{MorphIO-2.6.0 → MorphIO-2.6.2}/README.md

@@ -349,7 +349,7 @@ Morphology("myfile.asc", options=Option.no_duplicates|Option.nrn_order)
 
 <details>
   <summary>Click to expand!</summary>
-  
+
 MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
 https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
 
@@ -494,7 +494,7 @@ neuron.write('/my/out/file.h5')  # Has to be written to h5
 
 <details>
   <summary>Click to expand!</summary>
-  
+
 A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
 
 ```lisp
@@ -528,17 +528,40 @@ The following s-expressions are parsed:
     (9 10 11 6)
     )
     ```
-- An sexp with one of the following top level s-exp:
-  * Dot
-  * FilledCircle
-  * SnowFlake
-  * Asterisk
-  * OpenCircle
-  * OpenStar
-  * Flower
-  * OpenSquare
-  * FilledStar
-  * DoubleCircle
+- An sexp with one of the following top level regular expression:
+
+  - Dot[0-9]*
+  - Plus[0-9]*
+  - Cross[0-9]*
+  - Splat[0-9]*
+  - Flower[0-9]*
+  - Circle[0-9]*
+  - Flower[0-9]*
+  - TriStar[0-9]*
+  - OpenStar[0-9]*
+  - Asterisk[0-9]*
+  - SnowFlake[0-9]*
+  - OpenCircle[0-9]*
+  - ShadedStar[0-9]*
+  - FilledStar[0-9]*
+  - TexacoStar[0-9]*
+  - MoneyGreen[0-9]*
+  - DarkYellow[0-9]*
+  - OpenSquare[0-9]*
+  - OpenDiamond[0-9]*
+  - CircleArrow[0-9]*
+  - CircleCross[0-9]*
+  - OpenQuadStar[0-9]*
+  - DoubleCircle[0-9]*
+  - FilledSquare[0-9]*
+  - MalteseCross[0-9]*
+  - FilledCircle[0-9]*
+  - FilledDiamond[0-9]*
+  - FilledQuadStar[0-9]*
+  - OpenUpTriangle[0-9]*
+  - FilledUpTriangle[0-9]*
+  - OpenDownTriangle[0-9]*
+  - FilledDownTriangle[0-9]*
 
   Example:
   ```lisp
@@ -550,6 +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
@@ -571,6 +596,26 @@ assert_array_equal(pia.points,
 assert_array_equal(pia.diameters, [3, 4, 5, 6])
 ```
 
+⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+
+```python
+( (Color White)  ; [10,1]
+  (Dendrite)
+  ( -290.87  -113.09   -16.32     2.06)  ; Root
+  ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+  (
+    ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+    ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+    (Cross  ;  [3,3]
+      (Color Orange)
+      (Name "Marker 3")
+      ( -271.87  -121.14   -16.27     0.69)  ; 1
+      ( -269.34  -122.29   -15.48     0.69)  ; 2
+    )  ;  End of markers
+  )
+ )
+```
+
 </details>
 
 ### Tips

{MorphIO-2.6.0 → MorphIO-2.6.2}/src/readers/lex.cpp

@@ -162,17 +162,40 @@ class NeurolucidaLexer
         rules_.push("Dendrite", +Token::DENDRITE);
         rules_.push("CellBody", +Token::CELLBODY);
 
-        rules_.push("Dot", +Token::MARKER);
-        rules_.push("FilledCircle", +Token::MARKER);
-        rules_.push("SnowFlake", +Token::MARKER);
-        rules_.push("Asterisk", +Token::MARKER);
-        rules_.push("OpenCircle", +Token::MARKER);
-        rules_.push("OpenStar", +Token::MARKER);
-        rules_.push("Flower", +Token::MARKER);
-        rules_.push("OpenSquare", +Token::MARKER);
-        rules_.push("FilledStar", +Token::MARKER);
-        rules_.push("DoubleCircle", +Token::MARKER);
-        rules_.push("Circle[0-9]+", +Token::MARKER);
+        // The code snippet used to infer the marker list is available at:
+        // https://github.com/BlueBrain/MorphIO/pull/229
+        rules_.push("Dot[0-9]*", +Token::MARKER);
+        rules_.push("Plus[0-9]*", +Token::MARKER);
+        rules_.push("Cross[0-9]*", +Token::MARKER);
+        rules_.push("Splat[0-9]*", +Token::MARKER);
+        rules_.push("Flower[0-9]*", +Token::MARKER);
+        rules_.push("Circle[0-9]*", +Token::MARKER);
+        rules_.push("Flower[0-9]*", +Token::MARKER);
+        rules_.push("TriStar[0-9]*", +Token::MARKER);
+        rules_.push("OpenStar[0-9]*", +Token::MARKER);
+        rules_.push("Asterisk[0-9]*", +Token::MARKER);
+        rules_.push("SnowFlake[0-9]*", +Token::MARKER);
+        rules_.push("OpenCircle[0-9]*", +Token::MARKER);
+        rules_.push("ShadedStar[0-9]*", +Token::MARKER);
+        rules_.push("FilledStar[0-9]*", +Token::MARKER);
+        rules_.push("TexacoStar[0-9]*", +Token::MARKER);
+        rules_.push("MoneyGreen[0-9]*", +Token::MARKER);
+        rules_.push("DarkYellow[0-9]*", +Token::MARKER);
+        rules_.push("OpenSquare[0-9]*", +Token::MARKER);
+        rules_.push("OpenDiamond[0-9]*", +Token::MARKER);
+        rules_.push("CircleArrow[0-9]*", +Token::MARKER);
+        rules_.push("CircleCross[0-9]*", +Token::MARKER);
+        rules_.push("OpenQuadStar[0-9]*", +Token::MARKER);
+        rules_.push("DoubleCircle[0-9]*", +Token::MARKER);
+        rules_.push("FilledSquare[0-9]*", +Token::MARKER);
+        rules_.push("MalteseCross[0-9]*", +Token::MARKER);
+        rules_.push("FilledCircle[0-9]*", +Token::MARKER);
+        rules_.push("FilledDiamond[0-9]*", +Token::MARKER);
+        rules_.push("FilledQuadStar[0-9]*", +Token::MARKER);
+        rules_.push("OpenUpTriangle[0-9]*", +Token::MARKER);
+        rules_.push("FilledUpTriangle[0-9]*", +Token::MARKER);
+        rules_.push("OpenDownTriangle[0-9]*", +Token::MARKER);
+        rules_.push("FilledDownTriangle[0-9]*", +Token::MARKER);
 
         rules_.push("Generated", +Token::GENERATED);
         rules_.push("High", +Token::HIGH);

{MorphIO-2.6.0 → MorphIO-2.6.2}/src/readers/morphologyASC.cpp

@@ -47,7 +47,7 @@ bool is_end_of_section(Token id) {
 bool skip_sexp(size_t id) {
     return (id == +Token::WORD || id == +Token::COLOR || id == +Token::GENERATED ||
             id == +Token::HIGH || id == +Token::INCOMPLETE || id == +Token::LOW ||
-            id == +Token::NORMAL || id == +Token::FONT);
+            id == +Token::NORMAL || id == +Token::FONT || id == +Token::MARKER);
 }
 }  // namespace
 
@@ -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()));
             }

MorphIO-2.6.2/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)
+ )

{MorphIO-2.6.0 → MorphIO-2.6.2}/tests/test_2_neurolucida.py

@@ -1,4 +1,5 @@
 import os
+from itertools import product
 from pathlib import Path
 
 import morphio
@@ -12,9 +13,40 @@ from .utils import _test_asc_exception, assert_substring, captured_output, tmp_a
 
 DATA_DIR = Path(__file__).parent / 'data'
 
-NEUROLUCIDA_MARKERS = ['Dot', 'FilledCircle', 'SnowFlake', 'Asterisk', 'OpenCircle',
-                       'OpenStar', 'Flower', 'OpenSquare', 'FilledStar', 'DoubleCircle', 'Circle1']
-
+NEUROLUCIDA_MARKERS = [
+ 'Dot',
+ 'Plus',
+ 'Cross',
+ 'Splat',
+ 'Flower',
+ 'Circle',
+ 'Flower',
+ 'TriStar',
+ 'OpenStar',
+ 'Asterisk',
+ 'SnowFlake',
+ 'OpenCircle',
+ 'ShadedStar',
+ 'FilledStar',
+ 'TexacoStar',
+ 'MoneyGreen',
+ 'DarkYellow',
+ 'OpenSquare',
+ 'OpenDiamond',
+ 'CircleArrow',
+ 'CircleCross',
+ 'OpenQuadStar',
+ 'DoubleCircle',
+ 'FilledSquare',
+ 'MalteseCross',
+ 'FilledCircle',
+ 'FilledDiamond',
+ 'FilledQuadStar',
+ 'OpenUpTriangle',
+ 'FilledUpTriangle',
+ 'OpenDownTriangle',
+ 'FilledDownTriangle',
+ ]
 
 def test_soma():
     with tmp_asc_file('''("CellBody"
@@ -600,7 +632,8 @@ def test_string_markers():
 
 def test_neurolucida_markers():
     SIMPLE = Morphology(DATA_DIR / 'simple.asc')
-    for marker in NEUROLUCIDA_MARKERS[:1]:
+    for marker, suffix in product(NEUROLUCIDA_MARKERS, ['', '7', '123']):
+        marker += suffix
         with tmp_asc_file(f'''
 ({marker}
   (Color White)
@@ -667,3 +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))