pygmi 2.2.7__zip

pygmi-2.2.7/pygmi/raster/graphs.py

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+# -----------------------------------------------------------------------------
+# Name:        raster/graphs.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/>.
+# -----------------------------------------------------------------------------
+"""
+Plot Raster Data
+
+This module provides a variety of methods to plot raster data via the context
+menu. The following are supported:
+
+ * Correlation coefficients
+ * Images
+ * Surfaces
+ * Histograms
+"""
+
+import numpy as np
+from PyQt4 import QtGui, QtCore
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_qt4agg import FigureCanvas
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as \
+    NavigationToolbar
+import matplotlib.colors as mcolors
+
+
+class MyMplCanvas(FigureCanvas):
+    """
+    Canvas for the actual plot
+
+    Attributes
+    ----------
+    axes : matplotlib subplot
+    parent : parent
+        reference to the parent routine
+    """
+    def __init__(self, parent=None):
+        fig = Figure()
+        self.axes = fig.add_subplot(111)
+        self.parent = parent
+
+        FigureCanvas.__init__(self, fig)
+
+    def update_pcolor(self, data1, dmat):
+        """
+        Update the correlation coefficient plot
+
+        Parameters
+        ----------
+        data1 : PyGMI raster Data
+            raster dataset to be used in contouring
+        dmat : numpy array
+            dummy matrix of numbers to be plotted using pcolor
+        """
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111)
+        self.axes.pcolor(dmat)
+        self.axes.axis('scaled')
+        self.axes.set_title('Correlation Coefficients')
+        for i in range(len(data1)):
+            for j in range(len(data1)):
+                self.axes.text(i + .1, j + .4, format(float(dmat[i, j]),
+                                                      '4.2f'))
+        dat_mat = [i.dataid for i in data1]
+        self.axes.set_xticks(np.array(list(range(len(data1)))) + .5)
+
+        self.axes.set_xticklabels(dat_mat, rotation='vertical')
+        self.axes.set_yticks(np.array(list(range(len(data1)))) + .5)
+
+        self.axes.set_yticklabels(dat_mat, rotation='horizontal')
+        self.axes.set_xlim(0, len(data1))
+        self.axes.set_ylim(0, len(data1))
+#        self.figure.colorbar()
+
+        self.figure.tight_layout()
+        self.figure.canvas.draw()
+
+    def update_raster(self, data1, data2=None):
+        """
+        Update the raster plot
+
+        Parameters
+        ----------
+        data1 : PyGMI raster Data
+            raster dataset to be used in contouring
+        data2 : PyGMI point PData
+            points to be plotted over raster image
+        """
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111)
+
+        extent = (data1.tlx, data1.tlx + data1.cols * data1.xdim,
+                  data1.tly - data1.rows * data1.ydim, data1.tly)
+
+
+        rdata = self.axes.imshow(data1.data, extent=extent,
+                                 interpolation='nearest')
+
+        cbar = self.figure.colorbar(rdata)
+        try:
+            cbar.set_label(data1.units)
+        except AttributeError:
+            pass
+        self.axes.set_xlabel("Eastings")
+        self.axes.set_ylabel("Northings")
+
+        tmp = self.axes.get_yticks()
+        self.axes.set_yticklabels(tmp, rotation='horizontal')
+        tmp = self.axes.get_xticks()
+        self.axes.set_xticklabels(tmp, rotation='vertical')
+
+        self.figure.tight_layout()
+        self.figure.canvas.draw()
+
+    def update_rgb(self, data1):
+        """
+        Update the RGB plot
+
+        Parameters
+        ----------
+        data1 : PyGMI raster Data
+            raster dataset to be used
+        """
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111)
+
+        self.axes.imshow(data1.data)
+
+        self.figure.tight_layout()
+        self.figure.canvas.draw()
+
+    def update_hexbin(self, data1, data2):
+        """
+        Update the hexbin plot
+
+        Parameters
+        ----------
+        data1 : PyGMI raster Data
+            raster dataset to be used
+        data2 : PyGMI raster Data
+            raster dataset to be used
+        """
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111)
+        x = data1.copy()
+        y = data2.copy()
+        msk = np.logical_or(x.mask, y.mask)
+        x.mask = msk
+        y.mask = msk
+        x = x.compressed()
+        y = y.compressed()
+
+        xmin = x.min()
+        xmax = x.max()
+        ymin = y.min()
+        ymax = y.max()
+
+        hbin = self.axes.hexbin(x, y, bins='log')
+        self.axes.axis([xmin, xmax, ymin, ymax])
+        self.axes.set_title('Hexbin Plot')
+        cbar = self.figure.colorbar(hbin)
+        cbar.set_label('log10(N)')
+
+        self.figure.tight_layout()
+        self.figure.canvas.draw()
+
+    def update_wireframe(self, data):
+        """
+        Update the surface wireframe plot
+
+        Parameters
+        ----------
+        data : PyGMI raster Data
+            raster dataset to be used
+        """
+
+        x = data.tlx+np.arange(data.cols)*data.xdim+data.xdim/2
+        y = data.tly-np.arange(data.rows)*data.ydim-data.ydim/2
+        x, y = np.meshgrid(x, y)
+        z = data.data.copy()
+        if not np.ma.is_masked(z):
+            z = np.ma.array(z)
+
+        x = np.ma.array(x, mask=z.mask)
+        y = np.ma.array(y, mask=z.mask)
+
+        z[z.mask] = np.nan
+        z.mask = data.data.mask.copy()
+        cmap = plt.cm.jet
+        cmap.set_bad('w', 0.)
+        cmap.set_under('w', 0.)
+
+        lev = np.arange(z.min(), z.max(), 1)
+        norml = mcolors.BoundaryNorm(lev, 256)
+
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111, projection='3d')
+        ax = self.axes
+        ax.plot_surface(x, y, z, cmap=cmap, linewidth=0.1, norm=norml,
+                        shade=True)
+
+        ax.set_title('')
+        ax.set_xlabel("X")
+        ax.set_ylabel("Y")
+        ax.set_zlabel("Z")
+
+        self.figure.canvas.draw()
+
+    def update_hist(self, data1):
+        """
+        Update the hiostogram plot
+
+        Parameters
+        ----------
+        data1 : PyGMI raster Data
+            raster dataset to be used
+        """
+        self.figure.clear()
+        self.axes = self.figure.add_subplot(111)
+
+        dattmp = data1.data[data1.data.mask == 0].flatten()
+        self.axes.hist(dattmp, 50)
+        self.axes.set_title(data1.dataid, fontsize=12)
+        self.axes.set_xlabel("Data Value", fontsize=8)
+        self.axes.set_ylabel("Counts", fontsize=8)
+
+        self.figure.tight_layout()
+        self.figure.canvas.draw()
+
+
+class GraphWindow(QtGui.QDialog):
+    """
+    Graph Window - The QDialog window which will contain our image
+
+    Attributes
+    ----------
+    parent : parent
+        reference to the parent routine
+    """
+    def __init__(self, parent=None):
+        QtGui.QDialog.__init__(self, parent=None)
+        self.parent = parent
+
+        self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
+        self.setWindowTitle("Graph Window")
+
+        vbl = QtGui.QVBoxLayout(self)  # self is where layout is assigned
+        self.hbl = QtGui.QHBoxLayout()
+        self.mmc = MyMplCanvas(self)
+        mpl_toolbar = NavigationToolbar(self.mmc, self.parent)
+
+        self.combobox1 = QtGui.QComboBox()
+        self.combobox2 = QtGui.QComboBox()
+        self.label1 = QtGui.QLabel()
+        self.label2 = QtGui.QLabel()
+        self.label1.setText('Bands:')
+        self.label2.setText('Bands:')
+        self.hbl.addWidget(self.label1)
+        self.hbl.addWidget(self.combobox1)
+        self.hbl.addWidget(self.label2)
+        self.hbl.addWidget(self.combobox2)
+
+        vbl.addWidget(self.mmc)
+        vbl.addWidget(mpl_toolbar)
+        vbl.addLayout(self.hbl)
+
+        self.setFocus()
+
+        self.combobox1.currentIndexChanged.connect(self.change_band)
+        self.combobox2.currentIndexChanged.connect(self.change_band)
+
+    def change_band(self):
+        """ Combo box to choose band """
+        pass
+
+
+class PlotCCoef(GraphWindow):
+    """
+    Plot 2D Correlation Coeffiecients
+
+    Attributes
+    ----------
+    label1 : QLabel
+        reference to GraphWindow's label1
+    combobox1 : QComboBox
+        reference to GraphWindow's combobox1
+    label2 : QLabel
+        reference to GraphWindow's label2
+    combobox2 : QComboBox
+        reference to GraphWindow's combobox2
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    """
+    def __init__(self, parent):
+        GraphWindow.__init__(self, parent)
+        self.label1.hide()
+        self.combobox1.hide()
+        self.label2.hide()
+        self.combobox2.hide()
+        self.indata = {}
+        self.parent = parent
+
+    def change_band(self):
+        """ Combo box to choose band """
+        pass
+
+    def run(self):
+        """ Run """
+        self.show()
+        data = self.indata['Raster']
+
+        dummy_mat = [[self.corr2d(i.data, j.data) for j in data] for i in data]
+        dummy_mat = np.array(dummy_mat)
+
+        self.mmc.update_pcolor(data, dummy_mat)
+
+    def corr2d(self, dat1, dat2):
+        """
+        Calculate the 2D correlation
+
+        Parameters
+        ----------
+        dat1 : numpy array
+            dataset 1 for use in correlation calculation
+        dat2 : numpy array
+            dataset 2 for use in correlation calculation
+
+        Returns
+        -------
+        out : numpy array
+            array of correlation coefficients
+        """
+
+        out = None
+        if dat1.shape == dat2.shape:
+            mdat1 = dat1 - dat1.mean()
+            mdat2 = dat2 - dat2.mean()
+            numerator = (mdat1 * mdat2).sum()
+            denominator = np.sqrt((mdat1 ** 2).sum() * (mdat2 ** 2).sum())
+            out = numerator / denominator
+
+        return out
+
+
+class PlotRaster(GraphWindow):
+    """
+    Plot Raster Class
+
+    Attributes
+    ----------
+    label2 : QLabel
+        reference to GraphWindow's label2
+    combobox2 : QComboBox
+        reference to GraphWindow's combobox2
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    """
+    def __init__(self, parent):
+        GraphWindow.__init__(self, parent)
+        self.label2.hide()
+        self.combobox2.hide()
+        self.indata = {}
+        self.parent = parent
+
+    def change_band(self):
+        """ Combo box to choose band """
+        i = self.combobox1.currentIndex()
+        data2 = None
+        if 'Point' in self.indata:
+            data2 = self.indata['Point'][0]
+        if 'Raster' in self.indata:
+            data = self.indata['Raster']
+            self.mmc.update_raster(data[i], data2)
+        elif 'ProfPic' in self.indata:
+            data = self.indata['ProfPic']
+            self.mmc.update_rgb(data[i])
+
+    def run(self):
+        """ Run """
+        self.show()
+        if 'Raster' in self.indata:
+            data = self.indata['Raster']
+        elif 'Cluster' in self.indata:
+            data = self.indata['Cluster']
+        elif 'ProfPic' in self.indata:
+            data = self.indata['ProfPic']
+
+        for i in data:
+            self.combobox1.addItem(i.dataid)
+        self.change_band()
+
+
+class PlotSurface(GraphWindow):
+    """
+    Plot Raster Class
+
+    Attributes
+    ----------
+    label2 : QLabel
+        reference to GraphWindow's label2
+    combobox2 : QComboBox
+        reference to GraphWindow's combobox2
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    """
+    def __init__(self, parent):
+        GraphWindow.__init__(self, parent)
+        self.label2.hide()
+        self.combobox2.hide()
+        self.indata = {}
+        self.parent = parent
+
+    def change_band(self):
+        """ Combo box to choose band """
+        i = self.combobox1.currentIndex()
+        if 'Raster' in self.indata:
+            data = self.indata['Raster']
+            self.mmc.update_wireframe(data[i])
+
+    def run(self):
+        """ Run """
+        if 'Raster' in self.indata:
+            self.show()
+            data = self.indata['Raster']
+
+            for i in data:
+                self.combobox1.addItem(i.dataid)
+            self.change_band()
+
+
+class PlotScatter(GraphWindow):
+    """
+    Plot Hexbin Class. A Hexbin is a type of scatter plot which is raster.
+
+    Attributes
+    ----------
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    """
+    def __init__(self, parent):
+        GraphWindow.__init__(self, parent=None)
+        self.indata = {}
+        self.parent = parent
+
+    def change_band(self):
+        """ Combo box to choose band """
+        data = self.indata['Raster']
+        i = self.combobox1.currentIndex()
+        j = self.combobox2.currentIndex()
+        self.mmc.update_hexbin(data[i].data, data[j].data)
+
+    def run(self):
+        """ Run """
+        self.show()
+        data = self.indata['Raster']
+        for i in data:
+            self.combobox1.addItem(i.dataid)
+            self.combobox2.addItem(i.dataid)
+
+        self.label1.setText('X Band:')
+        self.label2.setText('Y Band:')
+        self.combobox1.setCurrentIndex(0)
+        self.combobox2.setCurrentIndex(1)
+
+
+class PlotHist(GraphWindow):
+    """
+    Plot Hist Class
+
+    Attributes
+    ----------
+    label2 : QLabel
+        reference to GraphWindow's label2
+    combobox2 : QComboBox
+        reference to GraphWindow's combobox2
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    """
+    def __init__(self, parent):
+        GraphWindow.__init__(self, parent)
+        self.label2.hide()
+        self.combobox2.hide()
+        self.indata = {}
+        self.parent = parent
+
+    def change_band(self):
+        """ Combo box to choose band """
+        data = self.indata['Raster']
+        i = self.combobox1.currentIndex()
+        self.mmc.update_hist(data[i])
+
+    def run(self):
+        """ Run """
+        self.show()
+        data = self.indata['Raster']
+        for i in data:
+            self.combobox1.addItem(i.dataid)
+
+        self.label1.setText('Band:')
+        self.combobox1.setCurrentIndex(0)
+        self.change_band()