Added graph utility.

Author: Dilawar Singh

.travis.yml

@@ -32,8 +32,3 @@ before_script:
 script:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.ci/travis_build_osx.sh; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.ci/travis_build_linux.sh; fi
-
-after_success:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then\
-      mkdir _sdist && cd _sdist && cmake .. && make sdist && make upload_test;\
-    fi

python/moose/graph_utils.py

@@ -1,39 +1,32 @@
 # -*- coding: utf-8 -*-
-"""graph_utils.py: Graph related utilties. It does not require networkx library.
-It writes files to be used with graphviz.
-
-Last modified: Sat Jan 18, 2014  05:01PM
+"""graph_utils.py:
 
+Some network analysis utilities.
 """
 
+from __future__ import print_function, division
+
 __author__           = "Dilawar Singh"
-__copyright__        = "Copyright 2013, NCBS Bangalore"
-__credits__          = ["NCBS Bangalore", "Bhalla Lab"]
-__license__          = "GPL"
-__version__          = "1.0.0"
+__copyright__        = "Copyright 2018-19, NCBS Bangalore"
 __maintainer__       = "Dilawar Singh"
 __email__            = "[email protected]"
-__status__           = "Development"
 
 import sys
+import hashlib
 from . import _moose
-import inspect
-from . import print_utils as debug
+from . import print_utils as pu
 import re
 
 pathPat = re.compile(r'.+?\[\d+\]$')
 
-def getMoosePaths(pat, isRoot=True):
-    ''' Return a list of paths for a given pattern. '''
-    if type(pat) != str:
-        pat = pat.path
-        assert type(pat) == str
-    moose_paths = [x.path for x in _moose.wildcardFind(pat)]
-    return moose_paths
-
 def writeGraphviz(filename=None, pat='/##[TYPE=Compartment]'):
-    '''This is  a generic function. It takes the the pattern, search for paths
-    and write a graphviz file.
+    '''Write Electrical network to a dot graph.
+
+    Params:
+
+    :filename: Default None. Write graphviz file to this path. If None, write to
+        stdout.
+    :pat: Compartment path. By default, search for all moose.Compartment.
     '''
 
     def fix(path):
@@ -44,14 +37,9 @@ def fix(path):
             path = path + '[0]'
         return path
 
-
-    pathList = getMoosePaths(pat)
     compList = _moose.wildcardFind(pat)
     if not compList:
-        debug.dump("WARN"
-                , "No compartment found"
-                , frame = inspect.currentframe()
-                )
+        pu.warn("No compartment found")
 
     dot = []
     dot.append("digraph G {")
@@ -83,3 +71,57 @@ def fix(path):
             graphviz.write(dot)
     return True
 
+def writeCRN(compt, path=None):
+    """Write chemical reaction network to a graphviz file.
+
+    :param compt: Given compartment.
+    :param filepath: Save to this filepath. If None, write to stdout.
+    """
+    dot = _crn(compt)
+    if path is None:
+        print(dot, file=sys.stdout)
+        return
+    with open(path, 'w') as f:
+        f.write(dot)
+
+def _fixLabel(name):
+    name = name.replace('*', 'star')
+    name = name.replace('.', '_')
+    return "\"{}\"".format(name)
+
+def _addNode(n, nodes, dot):
+    node = hashlib.sha224(n.path.encode()).hexdigest()
+    nodeType = 'pool'
+    if isinstance(n, _moose.Reac) or isinstance(n, _moose.ZombieReac):
+        node = 'r'+node
+        nodeType = 'reac'
+    else:
+        node = 'p'+node
+    if node in nodes:
+        return node
+
+    nLabel = n.name
+    if nodeType == 'reac':
+        nLabel = "kf=%g kb=%g"%(n.Kf, n.Kb)
+        dot.append('\t%s [label="%s", kf=%g, kb=%g, shape=rect]' % (
+            node, nLabel, n.Kf, n.Kb))
+    else:
+        dot.append('\t%s [label="%s", concInit=%g]' % (
+            node, nLabel, n.concInit))
+    return node
+
+def _crn(compt):
+    nodes = {}
+    reacs = _moose.wildcardFind(compt.path+'/##[TYPE=Reac]')
+    reacs += _moose.wildcardFind(compt.path+'/##[TYPE=ZombieReac]')
+    dot = ['digraph %s {\n\t overlap=false' % compt.name ]
+    for r in reacs:
+        rNode = _addNode(r, nodes, dot)
+        for s in r.neighbors['sub']:
+            sNode = _addNode(s, nodes, dot)
+            dot.append('\t%s -> %s' % (sNode, rNode))
+        for p in r.neighbors['prd']:
+            pNode = _addNode(p, nodes, dot)
+            dot.append('\t%s -> %s' % (rNode, pNode))
+    dot.append('}')
+    return '\n'.join(dot)

python/moose/graphutil.py

@@ -128,14 +128,23 @@ def plotTable(table, **kwargs):
         plt.legend(loc='best')
 
 def plotTables(tables, outfile=None, **kwargs):
-    """Plot a list of tables onto one figure only.
+    """Plot a dict of tables.
+
+    Each axis will be labeled with dict keys. The dict values must be
+    moose.Table/moose.Table2.
+
+    :param outfile: Default `None`. If given, plot will be saved to this filepath.
+    :param grid: A tuple with (cols, rows), default is (len(tables)//2+1, 2)
+    :param figsize: Size of figure (W, H) in inches. Default (10, 1.5*len(tables))
     """
     assert type(tables) == dict, "Expected a dict of moose.Table"
-    plt.figure(figsize=(10, 1.5*len(tables)))
+    plt.figure(figsize=kwargs.get('figsize', (10, 1.5*len(tables))))
     subplot = kwargs.get('subplot', True)
+    gridSize = kwargs.get('grid', (len(tables)//2+1, 2))
     for i, tname in enumerate(tables):
         if subplot:
-            plt.subplot(len(tables), 1, i+1)
+            assert gridSize[0] <= 9
+            plt.subplot(100*gridSize[0]+10*gridSize[1]+(i+1))
         yvec = tables[tname].vector
         xvec = np.linspace(0, moose.Clock('/clock').currentTime, len(yvec))
         plt.plot(xvec, yvec, label=tname)
@@ -152,9 +161,7 @@ def plotTables(tables, outfile=None, **kwargs):
         try:
             plt.savefig(outfile, transparent=True)
         except Exception as e:
-            pu.dump("WARN"
-                    , "Failed to save figure, plotting onto a window"
-                    )
+            pu.dump("WARN", "Failed to save figure. Errror %s"%e)
             plt.show()
     else:
         plt.show()

python/moose/plot_utils.py

@@ -87,7 +87,6 @@ def run(self):
         self.spawn(["ctest", "--output-on-failure", '-j2'])
         os.chdir(sdir_)
 
-
 class build_ext(_build_ext):
     user_options = [
             ('with-boost', None, 'Use Boost Libraries (OFF)')