Repository: PMEAL/OpenPNM
Pull request #1212 (2019-02-01 05:40:14)

Add PerGeos IO class
This adds functionality for loading AND saving between openpnm and avizo, which uses the PerGeos format.


Patch:
diff --git a/openpnm/io/PerGeos.py b/openpnm/io/PerGeos.py
new file mode 100644
index 000000000..08280605c
--- /dev/null
+++ b/openpnm/io/PerGeos.py
@@ -0,0 +1,201 @@
+import numpy
+import scipy as sp
+from openpnm.utils import logging
+from openpnm.io import GenericIO
+from openpnm.network import GenericNetwork
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+class PerGeos(GenericIO):
+    r"""
+    """
+
+    @classmethod
+    def save(cls, network=None, phases=[], filename=''):
+        r"""
+        """
+        # avoid printing truncated array
+        np.set_printoptions(threshold=np.inf)
+
+        project, network, phases = cls._parse_args(network=network,
+                                                   phases=phases)
+
+        # Ensure network has PerGeos' expected properties
+        network = network[0]
+        if 'pore.EqRadius' not in network.props():
+            try:
+                network['pore.EqRadius'] = network['pore.diameter']/2
+            except KeyError:
+                network['pore.EqRadius'] = np.ones([network.Np, ])
+
+        # Add phase properties to network, if any
+        for phase in phases:
+            for item in phase.keys(mode='props', deep=True):
+                temp = item.split('.', 1)
+                new_name = temp[0] + '.' + phase.name + '.' + temp[1]
+                network[new_name] = phase[item]
+
+        s = ["# Avizo 3D ASCII 3.0\n\n"]
+        s.append("define VERTEX " + str(network.Np) + '\n')
+        s.append("define EDGE " + str(network.Nt) + '\n')
+        s.append("define POINT " + str(2*network.Nt) + '\n\n')
+        s.append("Parameters {\n\tContentType \"HxPoreNetworkModel\"\n}\n\n")
+
+        types = {'b': 'int', 'i': 'int', 'f': 'float'}
+        typemap = {}
+        namemap = {}
+        shapemap = {}
+        propmap = {}
+        i = 1
+
+        NumEdgePoints = 1
+        for item in network.keys():
+            typemap[item] = types[str(network[item].dtype)[0]]
+            ncols = int(network[item].size/network[item].shape[0])
+            if ncols > 1:
+                shapemap[item] = '[' + str(ncols) + ']'
+            else:
+                shapemap[item] = ''
+            if item.startswith('pore'):
+                element = 'pore', 'VERTEX'
+            if item.startswith('throat'):
+                element = 'throat', 'EDGE'
+            n = item.replace(element[0] + '.', '').replace('.', '_').split('_')
+            n = ''.join([i[0].upper()+i[1:] for i in n if len(i)])
+            namemap[item] = n
+            temp = element[1] + " { " + typemap[item] + shapemap[item] + " "\
+                   + namemap[item] + " } @" + str(i) + '\n'
+
+            if temp.find('EdgeConnectivity') == -1:
+                # replaces openpnm tags with the mandatory am file's tags
+                if "Conns" in temp:
+                    temp = temp.replace("Conns", "EdgeConnectivity")
+                elif "Coords" in temp:
+                    temp = temp.replace("Coords", "VertexCoordinates")
+                s.append(temp)
+            propmap[item] = str(i)
+            if "NumEdgePoints" in temp:
+                NumEdgePoints = 0
+            i += 1
+
+        if NumEdgePoints:
+            temp = "EDGE { int NumEdgePoints" + " } @" + str(i) + '\n'
+            s.append(temp)
+            tempat = "@" + str(i) + '\n'
+            i += 1
+
+        # Add POINT data
+        s.append("POINT { float[3] EdgePointCoordinates } @" + str(i))
+        s.append("\n\n# Data section follows")
+        for item in network.keys():
+            data = network[item]
+            if item != 'throat.EdgeConnectivity':
+                s.append('\n\n@' + propmap[item] + '\n')
+                if shapemap[item] == '':
+                    data = sp.atleast_2d(data).T
+                if typemap[item] == 'float':
+                    formatter = {'float_kind': lambda x: "%.15E" % x}
+                else:
+                    formatter = None
+                if data.dtype == 'bool':
+                    data = data.astype(int)
+                d = sp.array2string(data, formatter=formatter)
+                s.append(d.replace('[', '').replace(']', '').replace('\n ', '\n'))
+
+        # Add POINT data
+        s.append('\n\n@' + str(i) + '\n')
+        formatter = {'float_kind': lambda x: "%.15E" % x}
+
+        conns = network['throat.conns']
+        d = sp.array2string(network['pore.coords'][conns], formatter=formatter)
+        for r in (('[', ''), (']', ''), ('\n\n', '\n'), ('\n  ', '\n'),
+                  ('\n ', '\n')):
+            d = d.replace(*r)
+        d += '\n'
+        s.append(d)
+
+        # Add NumEdgePoints
+        if NumEdgePoints:
+            s.append('\n\n' + tempat)
+            s.append(''.join(['2' + '\n']*network.Nt))
+
+        # Write to file
+        if filename == '':
+            filename = project.name
+        fname = cls._parse_filename(filename=filename, ext='am')
+        with open(fname, 'w') as f:
+            f.write(''.join(s))
+
+    @classmethod
+    def load(cls, filename, network=None):
+        r"""
+        """
+        net = {}
+
+        # ---------------------------------------------------------------------
+        # Parse the link1 file
+        filename = cls._parse_filename(filename=filename, ext='am')
+        with open(filename, mode='r') as f:
+            Np = None
+            Nt = None
+            while (Np is None) or (Nt is None):
+                s = f.readline()[:-1].split(' ')
+                if s[0] == 'define':
+                    if s[1] == 'VERTEX':
+                        Np = int(s[2])
+                    if s[1] == 'EDGE':
+                        Nt = int(s[2])
+
+            net = {}
+            propmap = {}
+            typemap = {}
+            shapemap = {}
+            while True:
+                s = f.readline()[:-1].split(' ')
+                if s[0] == 'VERTEX':
+                    dshape = [Np]
+                    if s[2].endswith(']'):
+                        ncols = int(s[2].split('[', 1)[1].split(']')[0])
+                        dshape.append(ncols)
+                    dtype = s[2].split('[')[0]
+                    temp = sp.zeros(dshape, dtype=dtype)
+                    net['pore.'+s[3]] = temp
+                    key = int(s[-1].replace('@', ''))
+                    propmap[key] = 'pore.'+s[3]
+                    typemap[key] = dtype
+                    shapemap[key] = dshape
+                elif s[0] == 'EDGE':
+                    dshape = [Nt]
+                    if s[2].endswith(']'):
+                        ncols = int(s[2].split('[', 1)[1].split(']')[0])
+                        dshape.append(ncols)
+                    dtype = s[2].split('[')[0]
+                    temp = sp.zeros(dshape, dtype=dtype)
+                    net['throat.'+s[3]] = temp
+                    key = int(s[-1].replace('@', ''))
+                    propmap[key] = 'throat.'+s[3]
+                    typemap[key] = dtype
+                    shapemap[key] = dshape
+                elif s[0] == '#':
+                    break
+
+            s = f.read().split('@')
+            for key in propmap.keys():
+                if key in s:
+                    data = s[key].split('\n')[1:]
+                    data = ' '.join(data)
+                    arr = sp.fromstring(data, dtype=typemap[key], sep=' ')
+                    arr = sp.reshape(arr, newshape=shapemap[key])
+                    net[propmap[key]] = arr
+            # End file parsing
+
+        net['pore.coords'] = net['pore.VertexCoordinates']
+        net['throat.conns'] = sp.sort(net['throat.EdgeConnectivity'], axis=1)
+
+        if network is None:
+            network = GenericNetwork()
+        network = cls._update_network(network=network, net=net)
+
+        return network.project
diff --git a/openpnm/io/__init__.py b/openpnm/io/__init__.py
index 72749f6c7..7830504a5 100644
--- a/openpnm/io/__init__.py
+++ b/openpnm/io/__init__.py
@@ -43,6 +43,8 @@ parameters.
 | JGF      | The JSON Graph Format is a schema specification of how to write  |
 |          | a graph object into JSON format                                  |
 +----------+------------------------------------------------------------------+
+| PerGeos  | The PerGeos format is used by the commercial software Avizo      |
++----------+------------------------------------------------------------------+
 | iMorph   | iMorph is a graphical interface program that provides some image |
 |          | analysis tools for porous media                                  |
 +----------+------------------------------------------------------------------+
@@ -65,6 +67,7 @@ from .MAT import MAT
 from .iMorph import iMorph
 from .MARock import MARock
 from .Statoil import Statoil
+from .PerGeos import PerGeos
 from .Pandas import Pandas
 from .HDF5 import HDF5
 from .XDMF import XDMF


Test patch:
diff --git a/tests/fixtures/PerGeos/flooded.am b/tests/fixtures/PerGeos/flooded.am
new file mode 100644
index 000000000..9ebc9d3ab
--- /dev/null
+++ b/tests/fixtures/PerGeos/flooded.am
@@ -0,0 +1,3810 @@
+# Avizo 3D ASCII 3.0
+
+
+define VERTEX 225
+define EDGE 301
+define POINT 602
+
+Parameters {
+    ContentType "HxPoreNetworkModel"
+}
+
+VERTEX { float[3] VertexCoordinates } @1
+VERTEX { float Volume } @2
+VERTEX { float Area } @3
+VERTEX { float EqRadius } @4
+VERTEX { int LabelID } @5
+VERTEX { float Pressure } @6
+EDGE { int[2] EdgeConnectivity } @7
+EDGE { int NumEdgePoints } @8
+EDGE { float Area } @9
+EDGE { float EqRadius } @10
+EDGE { float ChannelLength } @11
+EDGE { float FlowRatePerSec } @12
+POINT { float[3] EdgePointCoordinates } @13
+
+# Data section follows
+@1
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+
diff --git a/tests/fixtures/PerGeos/mandatory.am b/tests/fixtures/PerGeos/mandatory.am
new file mode 100644
index 000000000..60cb71982
--- /dev/null
+++ b/tests/fixtures/PerGeos/mandatory.am
@@ -0,0 +1,46 @@
+# Avizo 3D ASCII 3.0
+
+
+define VERTEX 3
+define EDGE 3
+define POINT 6
+
+Parameters {
+    ContentType "HxPoreNetworkModel"
+}
+
+VERTEX { float[3] VertexCoordinates } @1
+VERTEX { float EqRadius } @4
+EDGE { int[2] EdgeConnectivity } @6
+EDGE { int NumEdgePoints } @7
+POINT { float[3] EdgePointCoordinates } @11
+
+# Data section follows
+@1
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006 
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006 
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006 
+
+@4
+1.663660351562500e+004 
+1.150913769531250e+004 
+3.540010546875000e+004 
+
+@6
+2 0 
+1 0 
+2 1 
+
+@7
+2 
+2 
+2 
+
+@11
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006 
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006 
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006 
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006 
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006 
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006 
+
diff --git a/tests/fixtures/PerGeos/simplePNM.am b/tests/fixtures/PerGeos/simplePNM.am
new file mode 100644
index 000000000..e485466a6
--- /dev/null
+++ b/tests/fixtures/PerGeos/simplePNM.am
@@ -0,0 +1,81 @@
+# Avizo 3D ASCII 3.0
+
+
+define VERTEX 3
+define EDGE 3
+define POINT 6
+
+Parameters {
+    ContentType "HxPoreNetworkModel"
+}
+
+VERTEX { float[3] VertexCoordinates } @1
+VERTEX { float Volume } @2
+VERTEX { float Area } @3
+VERTEX { float EqRadius } @4
+VERTEX { int LabelID } @5
+EDGE { int[2] EdgeConnectivity } @6
+EDGE { int NumEdgePoints } @7
+EDGE { float Area } @8
+EDGE { float EqRadius } @9
+EDGE { float ChannelLength } @10
+POINT { float[3] EdgePointCoordinates } @11
+
+# Data section follows
+@1
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006
+
+@2
+1.928777747660800e+013
+6.385817878528000e+012
+1.858240417628160e+014
+
+@3
+5.384168448000000e+009
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+2.720774963200000e+010
+
+@4
+1.663660351562500e+004
+1.150913769531250e+004
+3.540010546875000e+004
+
+@5
+1
+2
+3
+
+@6
+2 0
+1 0
+2 1
+
+@7
+2
+2
+2
+
+@8
+1.372888192000000e+009
+2.792375400000000e+007
+7.901805600000000e+007
+
+@9
+2.090463867187500e+004
+2.981343261718750e+003
+5.015199707031250e+003
+
+@10
+4.766702734375000e+004
+5.021435156250000e+004
+7.100543750000000e+004
+
+@11
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006
+3.099916750000000e+006 1.505000625000000e+006 3.054984750000000e+006
+3.137905250000000e+006 1.513538375000000e+006 3.082482500000000e+006
+3.081143250000000e+006 1.471111250000000e+006 3.086930750000000e+006
diff --git a/tests/unit/io/CSVTest.py b/tests/unit/io/CSVTest.py
index 6b716f0ab..156fdeac6 100644
--- a/tests/unit/io/CSVTest.py
+++ b/tests/unit/io/CSVTest.py
@@ -78,6 +78,7 @@ class CSVTest:
         assert proj.network.name == self.net.name
         assert list(proj.phases().values())[0].name == self.phase_1.name
 
+
 if __name__ == '__main__':
     # All the tests in this file can be run with 'playing' this file
     t = CSVTest()
diff --git a/tests/unit/io/PerGeosTest.py b/tests/unit/io/PerGeosTest.py
new file mode 100644
index 000000000..8d9ba114e
--- /dev/null
+++ b/tests/unit/io/PerGeosTest.py
@@ -0,0 +1,66 @@
+import openpnm as op
+import pytest
+import py
+import os
+from pathlib import Path
+
+
+class PerGeosTest:
+
+    def setup_class(self):
+        ws = op.Workspace()
+        ws.clear()
+
+    def teardown_class(self):
+        ws = op.Workspace()
+        ws.clear()
+
+    def test_load_PerGeos_simple(self, tmpdir):
+        path = Path(os.path.realpath(__file__),
+                    '../../../fixtures/PerGeos/simplePNM.am')
+        project = op.io.PerGeos.load(path)
+        network = project.network
+        assert network.Np == 3
+        assert network.Nt == 3
+
+    def test_load_PerGeos_mandatory(self, tmpdir):
+        path = Path(os.path.realpath(__file__),
+                    '../../../fixtures/PerGeos/mandatory.am')
+        project = op.io.PerGeos.load(path)
+        network = project.network
+        assert network.Np == 3
+        assert network.Nt == 3
+
+    def test_load_PerGeos_flooded(self, tmpdir):
+        path = Path(os.path.realpath(__file__),
+                    '../../../fixtures/PerGeos/flooded.am')
+        project = op.io.PerGeos.load(path)
+        network = project.network
+        assert network.Np == 225
+        assert network.Nt == 301
+
+    def test_save_PerGeos(self, tmpdir):
+        net = op.network.Cubic(shape=[5, 5, 5])
+        water = op.phases.Water(network=net)
+        fname = tmpdir.join(net.project.name)
+        len_before = len(tmpdir.listdir())
+        op.io.PerGeos.save(network=net, phases=water, filename=fname)
+        print(tmpdir.listdir())
+        print(len(tmpdir.listdir()))
+        print(len_before)
+        assert len(tmpdir.listdir()) == (len_before + 1)
+        os.remove(fname.dirpath().join(net.project.name + '.am'))
+
+
+if __name__ == '__main__':
+    # All the tests in this file can be run with 'playing' this file
+    t = PerGeosTest()
+    self = t  # For interacting with the tests at the command line
+    t.setup_class()
+    for item in t.__dir__():
+        if item.startswith('test'):
+            print('running test: '+item)
+            try:
+                t.__getattribute__(item)()
+            except TypeError:
+                t.__getattribute__(item)(tmpdir=py.path.local())