Merge pull request #705 from the-virtual-brain/EBR-39

EBR-39: change contour function from phase plane

tvb_build/docker/requirements_group

@@ -12,7 +12,7 @@ pytest-cov
 pytest-xdist
 pytest-benchmark
 pytest-mock
-matplotlib==3.5.3
+matplotlib
 h5py
 typing
 BeautifulSoup4
@@ -28,13 +28,12 @@ jinja2
 nibabel>=4.0
 sqlalchemy
 alembic
-allensdk==0.16.3
+allensdk
 werkzeug
 gevent
 cherrypy
 MarkupSafe
 decorator
-tables==3.7.0
 pandas
 requests
 simplejson

tvb_framework/requirements.txt

@@ -12,7 +12,7 @@ pytest-cov
 pytest-xdist
 pytest-benchmark
 pytest-mock
-matplotlib==3.5.3
+matplotlib
 h5py
 typing
 BeautifulSoup4
@@ -28,13 +28,12 @@ jinja2
 nibabel>=4.0
 sqlalchemy
 alembic
-allensdk==0.16.3
+allensdk
 werkzeug
 gevent
 cherrypy
 MarkupSafe
 decorator
-tables==3.7.0
 pandas
 requests
 simplejson

tvb_framework/setup.py

@@ -41,10 +41,10 @@
 TVB_TEAM = "Mihai Andrei, Lia Domide, Stuart Knock, Bogdan Neacsa, Paula Prodan, Paula Sansz Leon, Marmaduke Woodman"
 
 TVB_INSTALL_REQUIREMENTS = ["alembic", "bctpy", "cherrypy", "docutils", "flask==2.3.3", "flask-restx",
-                            "formencode", "gevent", "h5py", "Jinja2", "matplotlib==3.5.3", "nibabel", "numpy", "pandas",
+                            "formencode", "gevent", "h5py", "Jinja2", "matplotlib", "nibabel", "numpy", "pandas",
                             "Pillow", "psutil", "python-keycloak", "requests", "requests-toolbelt>=0.10",
                             "scikit-learn", "scipy", "siibra==1.0a5", "simplejson", "six", "sqlalchemy",
-                            "tables==3.7.0", "tvb-data", "tvb-gdist", "tvb-library", "tvb-storage", "werkzeug"]
+                            "tvb-data", "tvb-gdist", "tvb-library", "tvb-storage", "werkzeug"]
 
 # Packaging tvb-framework with REST server inside
 with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as fd:

tvb_framework/tvb/adapters/visualizers/phase_plane_interactive.py

@@ -37,30 +37,24 @@
 # good idea to use a proper library for this.
 
 try:
-    from matplotlib import _cntr
-    # older matplotlib
-
-    def nullcline(x, y, z):
-        c = _cntr.Cntr(x, y, z)
-        # trace a contour
-        res = c.trace(0.0)
-        if not res:
-            return numpy.array([])
-        # result is a list of arrays of vertices and path codes
-        # (see docs for matplotlib.path.Path)
-        nseg = len(res) // 2
-        segments, codes = res[:nseg], res[nseg:]
-        return segments
-
-except ImportError:
     from matplotlib import _contour
-    # newer matplotlib >= 2.2
+    # old matplotlib
 
     def nullcline(x, y, z):
         c = _contour.QuadContourGenerator(x, y, z, None, True, 0)
         segments = c.create_contour(0.0)
         return segments[0]
 
+
+except ImportError:
+    import matplotlib.pyplot as plt
+    # new matplotlib, version 3.8.3
+
+    def nullcline(x, y, z):
+        c = plt.contour(x, y, z, levels=[0.0])
+        segments = c.collections[0].get_paths()
+        return segments
+
 # how much courser is the grid used to show the vectors
 GRID_SUBSAMPLE = 2
 # Set the resolution of the phase-plane and sample trajectories.
@@ -212,8 +206,8 @@ def compute_phase_plane(self):
         u, v = self._calc_phase_plane(self.default_sv, self.svx_ind, self.svy_ind, x, y)
         u = u[..., self.mode]  # project on active mode
         v = v[..., self.mode]
-        xnull = [{'path': segment.tolist(), 'nullcline_index': 0} for segment in nullcline(x, y, u)]
-        ynull = [{'path': segment.tolist(), 'nullcline_index': 1} for segment in nullcline(x, y, v)]
+        xnull = [{'path': segment.vertices.tolist(), 'nullcline_index': 0} for segment in nullcline(x, y, u)]
+        ynull = [{'path': segment.vertices.tolist(), 'nullcline_index': 1} for segment in nullcline(x, y, v)]
 
         # a courser mesh for the arrows
         xsmall = x[::GRID_SUBSAMPLE, ::GRID_SUBSAMPLE]