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script/__Lib/diffcalc/numjy/__init__.py

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+###
+# Copyright 2008-2011 Diamond Light Source Ltd.
+# This file is part of Diffcalc.
+#
+# Diffcalc 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.
+#
+# Diffcalc 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 Diffcalc.  If not, see <http://www.gnu.org/licenses/>.
+###
+
+try:
+    import Jama
+    from numjy import linalg
+    from numjy.jama_matrix_wrapper import matrix
+    JAMA = True
+except ImportError:
+    JAMA = False
+
+
+def hstack(list_of_column_matrices):
+    if not Jama:
+        raise Exception('Jama not available, use numpy directly')
+    ncol = len(list_of_column_matrices)
+    nrow = list_of_column_matrices[0].shape[0]
+    m = Jama.Matrix(nrow, ncol)
+    for c, column_matrix in enumerate(list_of_column_matrices):
+        m.setMatrix(0, nrow - 1, c, c, column_matrix.m)
+    return matrix(m)

script/__Lib/diffcalc/numjy/jama_matrix_wrapper.py

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+###
+# Copyright 2008-2011 Diamond Light Source Ltd.
+# This file is part of Diffcalc.
+#
+# Diffcalc 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.
+#
+# Diffcalc 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 Diffcalc.  If not, see <http://www.gnu.org/licenses/>.
+###
+
+import Jama
+
+
+class matrix(object):
+
+    def __init__(self, a):
+        if isinstance(a, Jama.Matrix):
+            self.m = a
+        elif isinstance(a, basestring):
+            l = []
+            for row in a.strip().split(';'):
+                l.append([float(element)
+                          for element in row.replace(',', ' ').split()])
+            self.m = Jama.Matrix(l)
+        elif isinstance(a, matrix):
+            self.m = Jama.Matrix(a.tolist())
+        elif isinstance(a, (list, tuple)):
+            if isinstance(a[0], (list, tuple)):
+                # a is a list of lists (not rigorous test!)
+                self.m = Jama.Matrix(a)
+            else:
+                # a is a row vector
+                self.m = Jama.Matrix([a])
+        else:
+            # give it a go
+            self.m = Jama.Matrix(a)
+
+    def __eq__(self, other):
+        nrow, ncol = self.shape
+        b = matrix(Jama.Matrix(nrow, ncol))
+        for i in range(nrow):
+            for j in range(ncol):
+                b[i, j] = self[i, j] == other[i, j]
+        return b
+
+    @property
+    def shape(self):
+        return self.m.getRowDimension(), self.m.getColumnDimension()
+
+    def __len__(self):
+        return self.m.getRowDimension()
+
+    def all(self):  # @ReservedAssignment
+        for row in self.m.array:
+            if not all(row):
+                return False
+        return True
+
+    def tolist(self):
+        l = []
+        nrow, ncol = self.shape
+        for i in range(nrow):
+            row = []
+            for j in range(ncol):
+                row.append(self[i, j])
+            l.append(row)
+        return l
+
+    def sum(self):  # @ReservedAssignment
+        return sum(sum(row) for row in self.m.array)
+
+    @property
+    def I(self):
+        return matrix(self.m.inverse())
+
+    @property
+    def T(self):
+        return matrix(self.m.transpose())
+
+    def _scaler(self, scaler):
+        return Jama.Matrix(self.shape[0], self.shape[1], scaler)
+
+    def __add__(self, other):
+        v = other.m if isinstance(other, matrix) else self._scaler(other)
+        return matrix(self.m.plus(v))
+
+    def __sub__(self, other):
+        v = other.m if isinstance(other, matrix) else self._scaler(other)
+        return matrix(self.m.minus(v))
+
+    def __mul__(self, other):
+        return matrix(self.m.times(other.m if isinstance(other, matrix) else
+                                   other))
+
+    def __div__(self, other):
+        # dividend = other.I if isinstance(other, matrix) else 1. /float(other)
+        return self.__mul__(1. / float(other))
+
+    def __getitem__(self, key):
+        i, j = key
+        return self.m.get(i, j)
+
+    def __setitem__(self, key, value):
+        i, j = key
+        self.m.set(i, j, value)
+
+    def __str__(self):
+        insides = ['  '.join([str(el) for el in row]) for row in self.tolist()]
+        return '[[' + ']\n ['.join(insides) + ']]'
+
+    def __repr__(self):
+        return 'matrix(' + '\n       '.join(self.__str__().split('\n')) + ')'

script/__Lib/diffcalc/numjy/linalg.py

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+###
+# Copyright 2008-2011 Diamond Light Source Ltd.
+# This file is part of Diffcalc.
+#
+# Diffcalc 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.
+#
+# Diffcalc 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 Diffcalc.  If not, see <http://www.gnu.org/licenses/>.
+###
+
+def norm(mat):
+    return mat.m.normF()