Recursive printing to view the inversion.

.travis.yml

@@ -4,7 +4,7 @@ python:
 virtualenv:
   system_site_packages: true
 before_install:
-  - sudo apt-get install -qq python-numpy python-scipy python-matplotlib libhdf5-dev
+  - sudo apt-get install -qq python-numpy python-scipy python-matplotlib
   - python SimPEG/setup.py
 # command to install dependencies
 install: "pip install -r requirements.txt --use-mirrors"

SimPEG/utils/Save.py

@@ -1,8 +1,12 @@
 import numpy as np
 import time
-import h5py
 import re
 
+try:
+    import h5py
+except Exception, e:
+    print 'Warning: SimPEG table needs h5py to be installed.'
+
 def natural_keys(text):
     '''
     alist.sort(key=natural_keys) sorts in human order
@@ -25,6 +29,52 @@ class SimPEGTable:
 
         self.inversions = hdf5InversionGroup(self,self.root.addGroup('inversions',soft=True))
 
+
+    def saveInversion(self, invObj, dataPath):
+
+        invObj._invNode = self.inversions.addGroup('%d'%self.numChildren)
+
+        # At the start of every iteration we will create a inversion iteration node.
+        def _doStartIteration_hdf5_inv(invObj):
+            invNodeIt = invObj._invNode.addGroup('%d'%(invObj._iter+1))
+            invNodeIt.attrs['complete'] = False
+            invNodeIt.attrs['time'] = time.time()
+            invObj._invNodeIt = invNodeIt
+        invObj.hook(_doStartIteration_hdf5_inv, overwrite=True)
+
+        def _doEndIteration_hdf5_inv(invObj):
+            invNodeIt = invObj._invNodeIt
+            invNodeIt.attrs['time'] = time.time() - invNodeIt.attrs['time']
+            invNodeIt.attrs['ctime'] = time.ctime()
+            invNodeIt.attrs['phi_d'] = invObj.phi_d
+            invNodeIt.attrs['phi_m'] = invObj.phi_m
+            invNodeIt.setArray('m', invObj.m)
+            invNodeIt.setArray('dpred', invObj.dpred)
+            invNodeIt.attrs['complete'] = True
+        invObj.hook(_doEndIteration_hdf5_inv, overwrite=True)
+
+        def _doStartIteration_hdf5_opt(optObj):
+            optNodeIt = optObj.parent._invNode.addGroup('%d.%d'%(optObj.parent._iter, optObj._iter))
+            optNodeIt.attrs['complete'] = False
+            optNodeIt.attrs['time'] = time.time()
+            optObj._optNodeIt = optNodeIt
+
+        invObj.opt.hook(_doStartIteration_hdf5_opt, overwrite=True)
+
+        def _doEndIteration_hdf5_opt(optObj, xt):
+            optNodeIt = optObj._optNodeIt
+            optNodeIt.attrs['time'] = time.time() - optNodeIt.attrs['time']
+            optNodeIt.attrs['ctime'] = time.ctime()
+            optNodeIt.setArray('m', xt)
+            optNodeIt.setArray('dpred', optObj.parent.dpred)
+            optNodeIt.setArray('searchDirection', optObj.searchDirection)
+            optNodeIt.attrs['complete'] = True
+        invObj.opt.hook(_doEndIteration_hdf5_opt, overwrite=True)
+
+        return invObj._invNode
+
+
+
 class hdf5Group(object):
     """Has some low level support for wrapping the native HDF5-Group class"""
 
@@ -93,54 +143,44 @@ class hdf5Group(object):
             child = self.childClass(self.T, child)
         return child
 
+    def show(self, pad='', maxDepth=1, depth=0):
+        """
+            Recursively show the structure of the database.
+
+            For example::
+
+                <hdf5InversionGroup group "/inversions" (1 member)>
+                    - <hdf5Inversion group "/inversions/0" (4 members)>
+                        - <hdf5InversionIteration group "/inversions/0/0.0" (3 members)>
+                        - <hdf5InversionIteration group "/inversions/0/0.1" (3 members)>
+                        - <hdf5InversionIteration group "/inversions/0/0.2" (3 members)>
+                        - <hdf5InversionIteration group "/inversions/0/0.3" (3 members)>
+        """
+        s = self.__str__()
+        pad += ' '*4
+        if maxDepth <= 0: print s
+        if depth >= maxDepth: return s
+
+        for c in self.children:
+            if issubclass(self[c].__class__, hdf5Group):
+                s += '\n%s- %s' % (pad, self[c].show(pad=pad,depth=depth+1,maxDepth=maxDepth))
+            else:
+                s += '\n%s- %s' % (pad, self[c].__str__())
+        if depth is 0:
+            print s
+        else:
+            return s
+
+    def __str__(self):
+        return '<%s "%s" (%d member%s)>' % (self.__class__.__name__, self.path, self.numChildren, '' if self.numChildren == 1 else 's')
+
+
 
 class hdf5InversionGroup(hdf5Group):
     def __init__(self, T, groupNode):
         hdf5Group.__init__(self, T, groupNode)
         self.childClass = hdf5Inversion
 
-    def saveInversion(self, invObj, dataPath):
-        invObj._invNode = self.addGroup('%d'%self.numChildren)
-
-        # At the start of every iteration we will create a inversion iteration node.
-        def _doStartIteration_hdf5_inv(invObj):
-            invNodeIt = invObj._invNode.addGroup('%d'%(invObj._iter+1))
-            invNodeIt.attrs['complete'] = False
-            invNodeIt.attrs['time'] = time.time()
-            invObj._invNodeIt = invNodeIt
-        invObj.hook(_doStartIteration_hdf5_inv, overwrite=True)
-
-        def _doEndIteration_hdf5_inv(invObj):
-            invNodeIt = invObj._invNodeIt
-            invNodeIt.attrs['time'] = time.time() - invNodeIt.attrs['time']
-            invNodeIt.attrs['ctime'] = time.ctime()
-            invNodeIt.attrs['phi_d'] = invObj.phi_d
-            invNodeIt.attrs['phi_m'] = invObj.phi_m
-            invNodeIt.setArray('m', invObj.m)
-            invNodeIt.setArray('dpred', invObj.dpred)
-            invNodeIt.attrs['complete'] = True
-        invObj.hook(_doEndIteration_hdf5_inv, overwrite=True)
-
-        def _doStartIteration_hdf5_opt(optObj):
-            optNodeIt = optObj.parent._invNode.addGroup('%d.%d'%(optObj.parent._iter, optObj._iter))
-            optNodeIt.attrs['complete'] = False
-            optNodeIt.attrs['time'] = time.time()
-            optObj._optNodeIt = optNodeIt
-
-        invObj.opt.hook(_doStartIteration_hdf5_opt, overwrite=True)
-
-        def _doEndIteration_hdf5_opt(optObj, xt):
-            optNodeIt = optObj._optNodeIt
-            optNodeIt.attrs['time'] = time.time() - optNodeIt.attrs['time']
-            optNodeIt.attrs['ctime'] = time.ctime()
-            optNodeIt.setArray('m', xt)
-            optNodeIt.setArray('dpred', optObj.parent.dpred)
-            optNodeIt.setArray('searchDirection', optObj.searchDirection)
-            optNodeIt.attrs['complete'] = True
-        invObj.opt.hook(_doEndIteration_hdf5_opt, overwrite=True)
-
-        return invObj._invNode
-
 
 class hdf5Inversion(hdf5Group):
     def __init__(self, T, groupNode):