morphio 2.5.1__tar.gz → 2.5.3__tar.gz

{MorphIO-2.5.1 → MorphIO-2.5.3}/CMakeLists.txt

@@ -6,7 +6,7 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_VERBOSE_MAKEFILE ON)
 
 option(BUILD_BINDINGS "Build the python bindings" ON)
-option(${PROJECT_NAME}_CXX_WARNINGS "Compile C++ with warnings" ON)
+option(MorphIO_CXX_WARNINGS "Compile C++ with warnings" ON)
 option(EXTERNAL_HIGHFIVE "Use HighFive from external source" OFF)
 option(MORPHIO_USE_DOUBLE "Use doubles instead of floats" OFF)
 

{MorphIO-2.5.1 → MorphIO-2.5.3}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.1
+Version: 2.5.3
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -31,6 +31,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
            * [Glia](#glia)
            * [Mitochondria](#mitochondria)
            * [Endoplasmic reticulum](#endoplasmic-reticulum)
+           * [NeuroLucida markers](#neurolucida-markers)
            * [Tips](#tips)
               * [Maximum number of warnings](#maximum-number-of-warnings)
         * [Specification](#specification)
@@ -129,6 +130,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         - Python mutable
         ```python
         from morphio import Morphology, Section, Soma
+        
         ```
         
         - C++ immutable
@@ -141,6 +143,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         - Python immutable
         ```python
         from morphio.mut import Morphology, Section, Soma
+        
         ```
         
         ### Read-only API
@@ -170,6 +173,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         ```Python
         from morphio.mut import Morphology, Section, Soma
+        
         ```
         
         ### Mutable Read/Write API
@@ -292,8 +296,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         Here is a simple example to create a morphology from scratch and writing it to disk
         
         ```python
+        from morphio import PointLevel, SectionType
         from morphio.mut import Morphology
-        from morphio import SectionType, PointLevel
         
         morpho = Morphology()
         morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
@@ -344,10 +348,15 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         Python:
         ```python
         from morphio import Morphology, Option
+        
         Morphology("myfile.asc", options=Option.no_duplicates|Option.nrn_order)
         ```
         
         ### Glia
+        
+        <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
         
@@ -362,10 +371,13 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         empty_glia = morphio.mut.GlialCell()
         mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
         ```
-        
+        </details>
         
         ### Mitochondria
         
+        <details>
+          <summary>Click to expand!</summary>
+        
         It is also possible to read and write mitochondria from/to the h5 files (*SWC and ASC are not supported*).
         As mitochondria can be represented as trees, one can define the concept of *mitochondrial section*
         similar to neuronal section and end up with a similar API. The morphology object has a
@@ -380,8 +392,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         _ `upstream_begin`: an upstream iterator
         
         ```python
-        from morphio.mut import Morphology
         from morphio import MitochondriaPointLevel, PointLevel, SectionType
+        from morphio.mut import Morphology
         
         morpho = Morphology()
         
@@ -429,8 +441,14 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
             print("Number of children: {}".format(len(mitochondrial_section.children)))
         ```
+        
+        </details>
+        
         ### Endoplasmic reticulum
         
+        <details>
+          <summary>Click to expand!</summary>
+        
         Endoplasmic reticulum can also be stored and written to H5 file.
         The specification is part of the [BBP morphology documentation](https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html)
         There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute is an array and each line
@@ -477,6 +495,91 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         neuron.write('/my/out/file.h5')  # Has to be written to h5
         ```
         
+        </details>
+        
+        ### NeuroLucida markers
+        
+        <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
+        ("pia"
+          (Closed)
+          (MBFObjectType 5)
+          (0 1 2 3)
+          (3 4 5 4)
+          (6 7 8 5)
+          (9 10 11 6)
+         )
+        ```
+        
+        This PR adds a `Morphology.markers` attribute that stores the markers found in the file.
+        A Marker object has 3 attributes:
+        - label
+        - points
+        - diameters.
+        
+        ##### Specification
+        
+        The following s-expressions are parsed:
+        - Any s-exp with a top level string. Like:
+            ```lisp
+            ("pia"
+            (Closed)
+            (MBFObjectType 5)
+            (0 1 2 3)
+            (3 4 5 4)
+            (6 7 8 5)
+            (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
+        
+          Example:
+          ```lisp
+          (FilledCircle
+          (Color RGB (64, 0, 128))
+          (Name "Marker 11")
+          (Set "axons")
+          ( -189.59    55.67    28.68     0.12)  ; 1
+          )  ;  End of markers
+          ```
+        
+        ##### Usage
+        
+        ```python
+        cell = Morphology(os.path.join(_path, 'pia.asc'))
+        all_markers = cell.markers
+        pia = m.markers[0]
+        
+        # fetch the label marker with the `label` attribute
+        assert_equal(pia.label, 'pia')
+        
+        # fetch the points with the `points` attribute
+        assert_array_equal(pia.points,
+                               [[0, 1, 2],
+                                [3, 4, 5],
+                                [6, 7, 8],
+                                [9, 10, 11]])
+        
+        # fetch the diameters with the `diameters` attribute
+        assert_array_equal(pia.diameters, [3, 4, 5, 6])
+        ```
+        
+        </details>
+        
         ### Tips
         #### Maximum number of warnings
         On can control the maximum number of warnings using the command:
@@ -495,6 +598,25 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         # Specification
         See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
         
+        
+        # H5v2
+        
+        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them with:
+        
+        ```bash
+        pip install morphio==2.5.1 morph-tool==2.3.0
+        ```
+        
+        and then:
+        ```python
+        # single file, OUTPUT must end with `.h5`
+        morph-tool convert file INPUTFILE OUTPUT
+        
+        # bulk conversion
+        morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+        ```
+        
         # Contributing
         If you want to improve the project or you see any issue, every contribution is welcome.
         Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.1 → MorphIO-2.5.3}/MorphIO.egg-info/SOURCES.txt

@@ -144,7 +144,11 @@ tests/data/nested_single_children.asc
 tests/data/neurite_wrong_root_point.swc
 tests/data/nrn-order-already-sorted.h5
 tests/data/nrn_ordering.swc
+tests/data/pia.asc
 tests/data/reversed_NRN_neurite_order.swc
+tests/data/sections-block.asc
+tests/data/simple-with-font.asc
+tests/data/simple-with-image-coord.asc
 tests/data/simple.asc
 tests/data/simple.swc
 tests/data/simple2.asc

{MorphIO-2.5.1 → MorphIO-2.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.1
+Version: 2.5.3
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -31,6 +31,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
            * [Glia](#glia)
            * [Mitochondria](#mitochondria)
            * [Endoplasmic reticulum](#endoplasmic-reticulum)
+           * [NeuroLucida markers](#neurolucida-markers)
            * [Tips](#tips)
               * [Maximum number of warnings](#maximum-number-of-warnings)
         * [Specification](#specification)
@@ -129,6 +130,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         - Python mutable
         ```python
         from morphio import Morphology, Section, Soma
+        
         ```
         
         - C++ immutable
@@ -141,6 +143,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         - Python immutable
         ```python
         from morphio.mut import Morphology, Section, Soma
+        
         ```
         
         ### Read-only API
@@ -170,6 +173,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         ```Python
         from morphio.mut import Morphology, Section, Soma
+        
         ```
         
         ### Mutable Read/Write API
@@ -292,8 +296,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         Here is a simple example to create a morphology from scratch and writing it to disk
         
         ```python
+        from morphio import PointLevel, SectionType
         from morphio.mut import Morphology
-        from morphio import SectionType, PointLevel
         
         morpho = Morphology()
         morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
@@ -344,10 +348,15 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         Python:
         ```python
         from morphio import Morphology, Option
+        
         Morphology("myfile.asc", options=Option.no_duplicates|Option.nrn_order)
         ```
         
         ### Glia
+        
+        <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
         
@@ -362,10 +371,13 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         empty_glia = morphio.mut.GlialCell()
         mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
         ```
-        
+        </details>
         
         ### Mitochondria
         
+        <details>
+          <summary>Click to expand!</summary>
+        
         It is also possible to read and write mitochondria from/to the h5 files (*SWC and ASC are not supported*).
         As mitochondria can be represented as trees, one can define the concept of *mitochondrial section*
         similar to neuronal section and end up with a similar API. The morphology object has a
@@ -380,8 +392,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         _ `upstream_begin`: an upstream iterator
         
         ```python
-        from morphio.mut import Morphology
         from morphio import MitochondriaPointLevel, PointLevel, SectionType
+        from morphio.mut import Morphology
         
         morpho = Morphology()
         
@@ -429,8 +441,14 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
             print("Number of children: {}".format(len(mitochondrial_section.children)))
         ```
+        
+        </details>
+        
         ### Endoplasmic reticulum
         
+        <details>
+          <summary>Click to expand!</summary>
+        
         Endoplasmic reticulum can also be stored and written to H5 file.
         The specification is part of the [BBP morphology documentation](https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html)
         There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute is an array and each line
@@ -477,6 +495,91 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         neuron.write('/my/out/file.h5')  # Has to be written to h5
         ```
         
+        </details>
+        
+        ### NeuroLucida markers
+        
+        <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
+        ("pia"
+          (Closed)
+          (MBFObjectType 5)
+          (0 1 2 3)
+          (3 4 5 4)
+          (6 7 8 5)
+          (9 10 11 6)
+         )
+        ```
+        
+        This PR adds a `Morphology.markers` attribute that stores the markers found in the file.
+        A Marker object has 3 attributes:
+        - label
+        - points
+        - diameters.
+        
+        ##### Specification
+        
+        The following s-expressions are parsed:
+        - Any s-exp with a top level string. Like:
+            ```lisp
+            ("pia"
+            (Closed)
+            (MBFObjectType 5)
+            (0 1 2 3)
+            (3 4 5 4)
+            (6 7 8 5)
+            (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
+        
+          Example:
+          ```lisp
+          (FilledCircle
+          (Color RGB (64, 0, 128))
+          (Name "Marker 11")
+          (Set "axons")
+          ( -189.59    55.67    28.68     0.12)  ; 1
+          )  ;  End of markers
+          ```
+        
+        ##### Usage
+        
+        ```python
+        cell = Morphology(os.path.join(_path, 'pia.asc'))
+        all_markers = cell.markers
+        pia = m.markers[0]
+        
+        # fetch the label marker with the `label` attribute
+        assert_equal(pia.label, 'pia')
+        
+        # fetch the points with the `points` attribute
+        assert_array_equal(pia.points,
+                               [[0, 1, 2],
+                                [3, 4, 5],
+                                [6, 7, 8],
+                                [9, 10, 11]])
+        
+        # fetch the diameters with the `diameters` attribute
+        assert_array_equal(pia.diameters, [3, 4, 5, 6])
+        ```
+        
+        </details>
+        
         ### Tips
         #### Maximum number of warnings
         On can control the maximum number of warnings using the command:
@@ -495,6 +598,25 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         # Specification
         See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
         
+        
+        # H5v2
+        
+        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them with:
+        
+        ```bash
+        pip install morphio==2.5.1 morph-tool==2.3.0
+        ```
+        
+        and then:
+        ```python
+        # single file, OUTPUT must end with `.h5`
+        morph-tool convert file INPUTFILE OUTPUT
+        
+        # bulk conversion
+        morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+        ```
+        
         # Contributing
         If you want to improve the project or you see any issue, every contribution is welcome.
         Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.1 → MorphIO-2.5.3}/README.md

@@ -24,6 +24,7 @@
    * [Glia](#glia)
    * [Mitochondria](#mitochondria)
    * [Endoplasmic reticulum](#endoplasmic-reticulum)
+   * [NeuroLucida markers](#neurolucida-markers)
    * [Tips](#tips)
       * [Maximum number of warnings](#maximum-number-of-warnings)
 * [Specification](#specification)
@@ -122,6 +123,7 @@ One important concept is that MorphIO is split into a *read-only* part and a *re
 - Python mutable
 ```python
 from morphio import Morphology, Section, Soma
+
 ```
 
 - C++ immutable
@@ -134,6 +136,7 @@ from morphio import Morphology, Section, Soma
 - Python immutable
 ```python
 from morphio.mut import Morphology, Section, Soma
+
 ```
 
 ### Read-only API
@@ -163,6 +166,7 @@ In Python the API is available under the `morphio.mut` module:
 
 ```Python
 from morphio.mut import Morphology, Section, Soma
+
 ```
 
 ### Mutable Read/Write API
@@ -285,8 +289,8 @@ for section in m.iter(first_root):
 Here is a simple example to create a morphology from scratch and writing it to disk
 
 ```python
+from morphio import PointLevel, SectionType
 from morphio.mut import Morphology
-from morphio import SectionType, PointLevel
 
 morpho = Morphology()
 morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
@@ -337,10 +341,15 @@ Morphology("myfile.asc", options=morphio::NO_DUPLICATES|morphio::NRN_ORDER)
 Python:
 ```python
 from morphio import Morphology, Option
+
 Morphology("myfile.asc", options=Option.no_duplicates|Option.nrn_order)
 ```
 
 ### Glia
+
+<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
 
@@ -355,10 +364,13 @@ immutable_glia = morphio.GlialCell("astrocyte.h5")
 empty_glia = morphio.mut.GlialCell()
 mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
 ```
-
+</details>
 
 ### Mitochondria
 
+<details>
+  <summary>Click to expand!</summary>
+
 It is also possible to read and write mitochondria from/to the h5 files (*SWC and ASC are not supported*).
 As mitochondria can be represented as trees, one can define the concept of *mitochondrial section*
 similar to neuronal section and end up with a similar API. The morphology object has a
@@ -373,8 +385,8 @@ _ `breadth_begin`: a breadth first iterator
 _ `upstream_begin`: an upstream iterator
 
 ```python
-from morphio.mut import Morphology
 from morphio import MitochondriaPointLevel, PointLevel, SectionType
+from morphio.mut import Morphology
 
 morpho = Morphology()
 
@@ -422,8 +434,14 @@ for mitochondrial_section in morpho.mitochondria.root_sections:
 
     print("Number of children: {}".format(len(mitochondrial_section.children)))
 ```
+
+</details>
+
 ### Endoplasmic reticulum
 
+<details>
+  <summary>Click to expand!</summary>
+
 Endoplasmic reticulum can also be stored and written to H5 file.
 The specification is part of the [BBP morphology documentation](https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html)
 There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute is an array and each line
@@ -470,6 +488,91 @@ reticulum.filament_counts = [4, 4]
 neuron.write('/my/out/file.h5')  # Has to be written to h5
 ```
 
+</details>
+
+### NeuroLucida markers
+
+<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
+("pia"
+  (Closed)
+  (MBFObjectType 5)
+  (0 1 2 3)
+  (3 4 5 4)
+  (6 7 8 5)
+  (9 10 11 6)
+ )
+```
+
+This PR adds a `Morphology.markers` attribute that stores the markers found in the file.
+A Marker object has 3 attributes:
+- label
+- points
+- diameters.
+
+##### Specification
+
+The following s-expressions are parsed:
+- Any s-exp with a top level string. Like:
+    ```lisp
+    ("pia"
+    (Closed)
+    (MBFObjectType 5)
+    (0 1 2 3)
+    (3 4 5 4)
+    (6 7 8 5)
+    (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
+
+  Example:
+  ```lisp
+  (FilledCircle
+  (Color RGB (64, 0, 128))
+  (Name "Marker 11")
+  (Set "axons")
+  ( -189.59    55.67    28.68     0.12)  ; 1
+  )  ;  End of markers
+  ```
+
+##### Usage
+
+```python
+cell = Morphology(os.path.join(_path, 'pia.asc'))
+all_markers = cell.markers
+pia = m.markers[0]
+
+# fetch the label marker with the `label` attribute
+assert_equal(pia.label, 'pia')
+
+# fetch the points with the `points` attribute
+assert_array_equal(pia.points,
+                       [[0, 1, 2],
+                        [3, 4, 5],
+                        [6, 7, 8],
+                        [9, 10, 11]])
+
+# fetch the diameters with the `diameters` attribute
+assert_array_equal(pia.diameters, [3, 4, 5, 6])
+```
+
+</details>
+
 ### Tips
 #### Maximum number of warnings
 On can control the maximum number of warnings using the command:
@@ -488,6 +591,25 @@ morphio.set_maximum_warnings(0)
 # Specification
 See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
 
+
+# H5v2
+
+Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+If you have morphologies in this format, you can convert them with:
+
+```bash
+pip install morphio==2.5.1 morph-tool==2.3.0
+```
+
+and then:
+```python
+# single file, OUTPUT must end with `.h5`
+morph-tool convert file INPUTFILE OUTPUT
+
+# bulk conversion
+morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+```
+
 # Contributing
 If you want to improve the project or you see any issue, every contribution is welcome.
 Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.1 → MorphIO-2.5.3}/binds/python/bind_immutable.cpp

@@ -46,6 +46,9 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly("annotations",
                                &morphio::Morphology::annotations,
                                "Returns a list of annotations")
+        .def_property_readonly("markers",
+                               &morphio::Morphology::markers,
+                               "Returns the list of NeuroLucida markers")
         .def_property_readonly("endoplasmic_reticulum",
                                &morphio::Morphology::endoplasmicReticulum,
                                "Returns the endoplasmic reticulum object")