pygmi 2.2.7__zip

pygmi-2.2.7/pygmi/test/__init__.py

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+"""
+Tests for PyGMI
+"""
+__all__ = ["pfmod"]
+from . import pfmod
+

pygmi-2.2.7/pygmi/test/pfmod.py

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+# -----------------------------------------------------------------------------
+# Name:        pfmod.py (part of PyGMI)
+#
+# Author:      Patrick Cole
+# E-Mail:      pcole@geoscience.org.za
+#
+# Copyright:   (c) 2013 Council for Geoscience
+# Licence:     GPL-3.0
+#
+# This file is part of PyGMI
+#
+# PyGMI is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyGMI is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------
+""" These are pfmod tests. Run this file from within this directory to do the
+tests """
+
+import numpy as np
+from pygmi.pfmod.grvmag3d import quick_model
+from pygmi.pfmod.grvmag3d import calc_field
+import matplotlib.pyplot as plt
+import pygmi.misc as ptimer
+
+
+def test(doplt=False):
+    """
+    Main test function
+
+    This test function compares the calculations performed by PyGMI to
+    calculations performed by a external software - namely mag2dc and grav2dc
+    by G.R.J Cooper.
+
+    A series of graphs are produced. If the test is successful, points and
+    lines on the graphs will coincide.
+    """
+    print('Testing modelling of gravity and potential field data')
+
+    # First initialise variables
+    x = []
+    z = []
+    xpos = []
+    g2dc = []
+    m2dc = []
+
+    # start to load in gravity data
+    gfile = open('Grav2dc_grav.txt')
+    tmp = gfile.read()
+    tmp2 = tmp.splitlines()
+
+    numx = get_int(tmp2, 2, 2)
+    cnrs = get_int(tmp2, 6, 4)
+    dens = get_float(tmp2, 6, 8) + 2.67
+    strike = get_float(tmp2, 7, 3)
+
+    for i in range(cnrs):
+        x.append(get_float(tmp2, 9+i, 0))
+        z.append(get_float(tmp2, 9+i, 1))
+
+    for i in range(numx):
+        xpos.append(get_float(tmp2, 11+cnrs+i, 0))
+        g2dc.append(get_float(tmp2, 11+cnrs+i, 1))
+
+    gfile.close()
+
+    # Convert to numpy and correct orientation of depths.
+    x = np.array(x)
+    z = -np.array(z)
+    xpos = np.array(xpos)
+    g2dc = np.array(g2dc)
+
+    # Start to load in magnetic data
+    mfile = open('Mag2dc_mag.txt')
+    tmp = mfile.read()
+    tmp2 = tmp.splitlines()
+
+    finc = get_float(tmp2, 4, 5)
+    fdec = get_float(tmp2, 4, 8)
+    mht = get_float(tmp2, 7, 5)
+    susc = get_float(tmp2, 12, 7)
+    minc = get_float(tmp2, 14, 9)
+    mdec = get_float(tmp2, 14, 12)
+    mstrength = get_float(tmp2, 14, 5)/(400*np.pi)
+
+    for i in range(numx):
+        m2dc.append(get_float(tmp2, 18+cnrs+i, 1))
+
+    mfile.close()
+
+    # Convert to numpy
+    m2dc = np.array(m2dc)
+
+    # for testing purposes the cube being modelled should have dxy = d_z to
+    # keep things simple
+    dxy = (xpos[1]-xpos[0])
+    d_z = 50
+    ypos = np.arange(-strike, strike, dxy)
+    zpos = np.arange(z.min(), 0, d_z)
+    xpos2 = np.arange(xpos.min(), xpos.max(), dxy)
+    numy = ypos.size
+    numz = zpos.size
+    tlx = xpos.min()
+    tly = ypos.max()
+    tlz = zpos.max()
+
+    # quick model initialises a model with all the variables we have defined.
+    ttt = ptimer.PTime()
+    lmod = quick_model(xpos2.size, numy, numz, dxy, d_z,
+                       tlx, tly, tlz, 0, 0, finc, fdec,
+                       ['Generic'], [susc], [dens],
+                       [minc], [mdec], [mstrength])
+    ttt.since_last_call('quick model')
+
+    # Create the actual model. It is a 3 dimensional vector with '1' where the
+    # body lies
+    for i in np.arange(x.min(), x.max(), dxy):
+        for j in np.arange(0, 2*strike, dxy):
+            for k in np.arange(abs(z).min()/d_z, abs(z).max()/d_z):
+                i2 = int(i/dxy)
+                j2 = int(j/dxy)
+                k2 = int(k)
+                lmod.lith_index[i2, j2, k2] = 1
+
+    ttt.since_last_call('model create')
+
+    # Calculate the gravity
+    calc_field(lmod)
+    gdata = lmod.griddata['Calculated Gravity'].data[numy/2].copy()
+    ttt.since_last_call('gravity calculation')
+
+    # Change to observation height to 100 meters and calculate magnetics
+    lmod.mht = mht
+    calc_field(lmod, magcalc=True)
+
+    mdata = lmod.griddata['Calculated Magnetics'].data[numy/2]
+
+    ttt.since_last_call('magnetic calculation')
+
+    if doplt:
+        # Display results
+        _, ax1 = plt.subplots()
+        ax1.set_xlabel('Distance (m)')
+        ax1.plot(xpos2+dxy/2, gdata, 'r', label='PyGMI')
+        ax1.plot(xpos, g2dc, 'r.', label='Grav2DC')
+        ax1.set_ylabel('mGal')
+        ax1.legend(loc='upper left', shadow=True)
+
+        ax2 = ax1.twinx()
+        ax2.plot(xpos2+dxy/2, mdata, 'b', label='PyGMI')
+        ax2.plot(xpos, m2dc, 'b.', label='Mag2DC')
+        ax2.set_ylabel('nT')
+        ax2.legend(loc='upper right', shadow=True)
+        plt.show()
+
+#    print(mdata[:-1]-m2dc[2::2])
+#    np.testing.assert_almost_equal(gdata[:-1], g2dc[2::2], 1)
+#    np.testing.assert_almost_equal(mdata[:-1], m2dc[2::2], 1)
+
+
+def get_int(tmp, row, word):
+    """
+    Gets an int from a list of strings.
+
+    Parameters
+    ----------
+    tmp : list
+        list of strings
+    row : int
+        row in list to extract. First row is 0
+    word : int
+        word to extract from row. First word is 0
+
+    Returns
+    -------
+     output : int
+         return an integer from the row.
+    """
+    return int(tmp[row].split()[word])
+
+
+def get_float(tmp, row, word):
+    """
+    Gets a float from a list of strings.
+
+    Parameters
+    ----------
+    tmp : list
+        list of strings
+    row : int
+        row in list to extract. First row is 0
+    word : int
+        word to extract from row. First word is 0
+
+    Returns
+    -------
+     output : float
+         return a float from the row.
+    """
+    return float(tmp[row].split()[word])
+
+
+if __name__ == "__main__":
+    test(True)

pygmi-2.2.7/pygmi/test/tests.py

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+# -----------------------------------------------------------------------------
+# Name:        pfmod.py (part of PyGMI)
+#
+# Author:      Patrick Cole
+# E-Mail:      pcole@geoscience.org.za
+#
+# Copyright:   (c) 2013 Council for Geoscience
+# Licence:     GPL-3.0
+#
+# This file is part of PyGMI
+#
+# PyGMI is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyGMI is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------
+""" These are tests. Run this file from within this directory to do the
+tests """
+
+import numpy as np
+import pfmod
+import nose
+
+
+def test():
+    """ Test Routine """
+    pfmod.test()
+
+if __name__ == "__main__":
+    # doctest.testmod(pygmi.raster)
+    nose.run()

pygmi-2.2.7/pygmi/vector/__init__.py

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+"""
+Vector data routines
+"""
+__all__ = ["datatypes", "iodefs", "graphs"]
+from . import datatypes
+from . import iodefs
+from . import graphs

pygmi-2.2.7/pygmi/vector/datatypes.py

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+# -----------------------------------------------------------------------------
+# Name:        datatypes.py (part of PyGMI)
+#
+# Author:      Patrick Cole
+# E-Mail:      pcole@geoscience.org.za
+#
+# Copyright:   (c) 2013 Council for Geoscience
+# Licence:     GPL-3.0
+#
+# This file is part of PyGMI
+#
+# PyGMI is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyGMI is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------
+""" Module for vector data types """
+
+import numpy as np
+
+
+class PData(object):
+    """
+    Class for point data
+
+    Attributes
+    ----------
+    xdata : numpy array
+        array of x coordinates
+    ydata : numpy array
+        array of y coordinates
+    zdata : numpy array
+        array of z coordinates
+    dataid : str
+        data description
+    """
+
+    def __init__(self):
+        self.xdata = np.array([])
+        self.ydata = np.array([])
+        self.zdata = np.array([])
+        self.dataid = ""
+
+
+class VData(object):
+    """
+    Class for Vector data. Typically used for storage of shape files.
+
+    Attributes
+    ----------
+    crds : list
+        List of coordinates
+    attrib : list
+        list of dictionaries, where each dictionary is the column in a table
+    dataid : str
+        data description
+    dtype : str
+        type of data - Line, Point, Poly
+    """
+    def __init__(self):
+        # Since each line can have variable amount of points, it is best to
+        # store in a list
+        self.crds = []
+        self.attrib = [{}]
+        self.dataid = ""
+        self.dtype = ""