pygmi 2.2.7__zip

pygmi-2.2.7/pygmi/raster/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/>.
+# -----------------------------------------------------------------------------
+""" Class for raster data types and conversion routines"""
+
+import numpy as np
+
+
+def numpy_to_pygmi(data):
+    """
+    Converts an MxN numpy array into a PyGMI data object
+
+    Parameters
+    ----------
+    data : numpy array
+        MxN array
+
+    Returns
+    -------
+    tmp : Data
+        PyGMI raster dataset
+    """
+    if data.ndim != 2:
+        print("Error: you need 2 dimensions")
+        return
+    tmp = Data()
+    if np.ma.isMaskedArray(data):
+        tmp.data = data
+    else:
+        tmp.data.data = data
+    tmp.ydim, tmp.xdim = data.shape
+
+    return tmp
+
+
+def pygmi_to_numpy(tmp):
+    """
+    Converts a PyGMI data object into an MxN numpy array
+
+    Parameters
+    ----------
+    tmp : Data
+        PyGMI raster dataset
+
+    Returns
+    -------
+    array : numpy array
+        MxN numpy array
+    """
+    return np.array(tmp.data)
+
+
+class Data(object):
+    """
+    PyGMI Data Object
+
+    Attributes
+    ----------
+    data : numpy masked array
+        array to contain raster data
+    tlx : float
+        Top Left X coordinate of raster grid
+    tly : float
+        Top Left Y coordinate of raster grid
+    xdim : float
+        x-dimension of grid cell
+    ydim : float
+        y-dimension of grid cell
+    nrofbands : int
+        number of raster bands
+    dataid : str
+        band name or id
+    rows : int
+        number of rows for each raster grid/band
+    cols : int
+        number of columns for each raster grid/band
+    nullvalue : float
+        grid null or nodata value
+    norm : dictionary
+        normalized data
+    gtr : tuple
+        projection information
+    wkt : str
+        projection information
+    units : str
+        description of units to be used with color bars
+    """
+    def __init__(self):
+        self.data = np.ma.array([])
+        self.tlx = 0.0  # Top Left X coordinate
+        self.tly = 0.0  # Top Left Y coordinate
+        self.xdim = 1.0
+        self.ydim = 1.0
+        self.nrofbands = 1
+        self.dataid = ''
+        self.rows = -1
+        self.cols = -1
+        self.nullvalue = 1e+20
+        self.norm = {}
+        self.gtr = (0.0, 1.0, 0.0, 0.0, -1.0)
+        self.wkt = ''
+        self.units = ''

pygmi-2.2.7/pygmi/raster/equation_editor.py

@@ -0,0 +1,256 @@
+# -----------------------------------------------------------------------------
+# Name:        equation_editor.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/>.
+# -----------------------------------------------------------------------------
+""" This is the function which calls the equation editor """
+
+from PyQt4 import QtGui, QtCore
+import numpy as np
+import copy
+import numexpr as ne
+import pygmi.raster.dataprep as dataprep
+
+
+class EquationEditor(QtGui.QDialog):
+    """
+    Equation Editor
+
+    This class allows the input of equations using raster datasets as
+    variables. This is commonly done in remote sensing applications, where
+    there is a requirement for band ratioing etc. It uses the numexpr library.
+
+    Attributes
+    ----------
+    parent : parent
+        reference to the parent routine
+    indata : dictionary
+        dictionary of input datasets
+    outdata : dictionary
+        dictionary of output datasets
+    equation : str
+        string with the equation in it
+    bands : dictionary
+        dictionary of bands
+    bandsall : list
+        list of all bands
+    """
+    def __init__(self, parent=None):
+        QtGui.QDialog.__init__(self, parent)
+
+        self.indata = {}
+        self.outdata = {}
+        self.parent = parent
+        self.equation = ''
+        self.bands = {}
+        self.bandsall = []
+        self.localdict = {}
+
+        self.bands['all data'] = 'iall'
+
+        self.combobox = QtGui.QComboBox()
+
+        self.textbrowser = QtGui.QTextEdit()
+        self.textbrowser2 = QtGui.QTextBrowser()
+        self.label = QtGui.QLabel()
+
+        self.setupui()
+
+    def textchanged(self):
+        """ Text Changed """
+        self.equation = self.textbrowser.toPlainText()
+
+    def setupui(self):
+        """ Setup UI """
+        gridlayout = QtGui.QGridLayout(self)
+        buttonbox = QtGui.QDialogButtonBox()
+        label_2 = QtGui.QLabel()
+
+        self.textbrowser.setEnabled(True)
+        self.resize(600, 480)
+
+        buttonbox.setOrientation(QtCore.Qt.Horizontal)
+        buttonbox.setStandardButtons(buttonbox.Cancel | buttonbox.Ok)
+
+        ptmp = self.textbrowser2.palette()
+        ptmp.setColor(0, 9, ptmp.color(10))
+        ptmp.setColor(1, 9, ptmp.color(10))
+        ptmp.setColor(2, 9, ptmp.color(10))
+        self.textbrowser2.setPalette(ptmp)
+        self.textbrowser2.setFrameShape(QtGui.QFrame.NoFrame)
+
+        self.setWindowTitle("Equation Editor")
+        self.label.setText(": iall")
+        label_2.setText("Output Equation:")
+        self.textbrowser.setText('iall')
+        tmp = ('<h1>Instructions:</h1>'
+               '<p>Equation editor uses the numexpr library. Use the variables'
+               ' iall, i1, i2 etc in formulas. The combobox above shows which '
+               'band is assigned to each variable.</p>'
+               '<h2>Examples</h2>'
+               '<p>Sum:</p>'
+               '<p>    i1 + 1000</p>'
+               '<p>Threshold between values 1 and 98, substituting -999 as a '
+               'nodata value:</p>'
+               '<p>    where((i1 &gt; 1) &amp; (i1 &lt; 98) , i1, -999)</p>'
+               '<h2>Commands</h2>'
+               '<ul>'
+               ' <li> Logical operators: &amp;, |, ~</li>'
+               ' <li> Comparison operators: &lt;, &lt;=, ==, !=, &gt;=, &gt;</li>'
+               ' <li> Arithmetic operators: +, -, *, /, **, %, <<, >></li>'
+               ' <li> where(bool, number1, number2) : number1 if the bool '
+               'condition is true, number2 otherwise.</li>'
+               ' <li> sin, cos, tan, arcsin, arccos, arctan, '
+               'sinh, cosh, tanh, arctan2, arcsinh, arccosh, arctanh</li>'
+               ' <li> log, log10, log1p, exp, expm1</li>'
+               ' <li> sqrt, abs</li>'
+               '</ul>')
+        self.textbrowser2.setHtml(tmp)
+
+        gridlayout.addWidget(label_2, 0, 0, 1, 1)
+        gridlayout.addWidget(self.textbrowser, 1, 0, 1, 2)
+        gridlayout.addWidget(self.combobox, 4, 0, 1, 1)
+        gridlayout.addWidget(self.label, 4, 1, 1, 1)
+        gridlayout.addWidget(self.textbrowser2, 5, 0, 1, 2)
+        gridlayout.addWidget(buttonbox, 6, 0, 1, 2)
+
+        self.combobox.currentIndexChanged.connect(self.combo)
+        self.textbrowser.textChanged.connect(self.textchanged)
+        buttonbox.accepted.connect(self.accept)
+        buttonbox.rejected.connect(self.reject)
+
+    def combo(self):
+        """ update combo information """
+        txt = self.combobox.currentText()
+        if txt == '':
+            return
+        self.label.setText(': '+self.bands[txt])
+
+    def eq_fix(self):
+        """ Corrects names in equation to variable names """
+        neweq = str(self.equation)
+        neweq = neweq.replace('ln', 'log')
+        neweq = neweq.replace('^', '**')
+
+        return neweq
+
+    def settings(self):
+        """ Settings """
+        self.combobox.clear()
+        self.combobox.addItem('all data')
+
+        self.bandsall = []
+
+        if 'Cluster' in self.indata:
+            intype = 'Cluster'
+        elif 'Raster' in self.indata:
+            intype = 'Raster'
+        else:
+            self.parent.showprocesslog('No raster data')
+            return
+
+        indata = dataprep.merge(self.indata[intype])
+
+        mask = indata[-1].data.mask
+        for i in indata:
+            mask = np.logical_or(mask, i.data.mask)
+        for i in indata:
+            i.data.mask = mask
+
+        self.localdict = {}
+        j = 0
+        for i in indata:
+            j += 1
+            self.localdict['i'+str(j)] = i.data
+            self.bands[i.dataid] = 'i'+str(j)
+            self.bandsall.append(i.data)
+            self.combobox.addItem(i.dataid)
+        self.localdict['iall'] = np.ma.array(self.bandsall)
+
+        self.bandsall = np.ma.array(self.bandsall)
+
+        temp = self.exec_()
+
+        if temp == 0:
+            return
+
+        self.equation = self.textbrowser.toPlainText()
+
+        if self.equation == '':
+            return
+
+        neweq = self.eq_fix()
+
+        findat = ne.evaluate(neweq, self.localdict)
+        outdata = []
+
+        if np.size(findat) == 1:
+            QtGui.QMessageBox.warning(
+                self.parent, 'Warning',
+                ' Nothing processed! Your equation outputs a single ' +
+                'value instead of a minimum of one band.',
+                QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
+            return
+        elif len(findat.shape) == 2:
+            masktmp = np.logical_or(indata[0].data.mask, np.isnan(findat))
+            outdata = [copy.copy(indata[0])]
+            outdata[0].data = np.ma.array(findat, mask=masktmp)
+            outdata[0].dataid = 'equation output'
+        else:
+            for i in range(len(findat)):
+                masktmp = np.logical_or(indata[i].data.mask,
+                                        np.isnan(findat[i]))
+                outdata.append(copy.copy(indata[i]))
+                outdata[-1].data = np.ma.array(findat[i], mask=masktmp)
+
+        self.outdata[intype] = outdata
+
+        return True
+
+
+def hmode(data):
+    """
+    Mode - this uses a histogram to generate a fast mode estimate
+
+    Parameters
+    ----------
+    data : list
+        list of values to generate the mode from.
+
+    Returns
+    -------
+    mode2 : float
+        mode value
+    """
+    mmin = np.min(data)
+    mmax = np.max(data)
+    for _ in range(2):
+        mhist = np.histogram(data, 255, range=(mmin, mmax))
+        mtmp = mhist[0].tolist()
+        mind = mtmp.index(max(mtmp))
+        mmin = mhist[1][mind]
+        mmax = mhist[1][mind+1]
+
+    mode2 = (mmax-mmin)/2 + mmin
+#        mcnt = mhist[0][mind]
+
+    return mode2