Ignore:
Timestamp:
Jun 30, 2009, 2:07:41 PM (16 years ago)
Author:
ole
Message:

Merged numpy branch back into the trunk.

In ~/sandpit/anuga/anuga_core/source
svn merge -r 6246:HEAD ../../branches/numpy .

In ~/sandpit/anuga/anuga_validation
svn merge -r 6417:HEAD ../branches/numpy_anuga_validation .

In ~/sandpit/anuga/misc
svn merge -r 6809:HEAD ../branches/numpy_misc .

For all merges, I used numpy version where conflicts existed

The suites test_all.py (in source/anuga) and validate_all.py passed using Python2.5 with numpy on my Ubuntu Linux box.

Location:
anuga_core/source/anuga/mesh_engine
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • anuga_core/source/anuga/mesh_engine/mesh_engine.py

    r6155 r7276  
    1111#import anuga.mesh_engine.list_dic as triang
    1212
    13 import Numeric as num
     13import numpy as num
    1414
    1515from anuga.utilities.numerical_tools import ensure_numeric
    … …  
    4646       
    4747    try:
    48         points =  ensure_numeric(points, num.Float)
     48        points =  ensure_numeric(points, num.float)
    4949    except ValueError:
    5050        msg = 'ERROR: Inconsistent points array.'
    … …  
    6060       
    6161    try:
    62         # If Int is used, instead of Int32, it fails in Linux
    63         segments = ensure_numeric(segments, num.Int32)
     62        # If num.int is used, instead of num.int32, it fails in Linux
     63        segments = ensure_numeric(segments, num.int32)
    6464       
    6565    except ValueError:
    … …  
    7272       
    7373    try:
    74         holes = ensure_numeric(holes, num.Float)
     74        holes = ensure_numeric(holes, num.float)
    7575    except ValueError:
    7676        msg = 'ERROR: Inconsistent holess array.'
    … …  
    8080    regions = add_area_tag(regions)
    8181    try:
    82         regions = ensure_numeric(regions, num.Float)
     82        regions = ensure_numeric(regions, num.float)
    8383    except  (ValueError, TypeError):
    8484        msg = 'ERROR: Inconsistent regions array.'
    … …  
    9090   
    9191    try:
    92         pointatts = ensure_numeric(pointatts, num.Float)
     92        pointatts = ensure_numeric(pointatts, num.float)
    9393    except (ValueError, TypeError):
    9494        msg = 'ERROR: Inconsistent point attributes array.'
    … …  
    103103   
    104104    try:
    105         segatts = ensure_numeric(segatts, num.Int32)
     105        segatts = ensure_numeric(segatts, num.int32)
    106106    except ValueError:
    107107        msg = 'ERROR: Inconsistent point attributes array.'

  • anuga_core/source/anuga/mesh_engine/mesh_engine_c_layer.c

    r4917 r7276  
    88
    99    This code interfaces pmesh directly with "triangle", a general       
    10     purpose triangulation code. In doing so, Python Numeric data structures
     10    purpose triangulation code. In doing so, Python numeric data structures
    1111     are passed to C for  use by "triangle" and the results are then         
    1212    converted back. This was accomplished using the Python/C API.           
    … …  
    6060#include "Python.h"
    6161
     62#include "util_ext.h"
     63#include "numpy_shim.h"
     64
     65
    6266//#define PY_ARRAY_UNIQUE_SYMBOL API_YEAH
    6367
    6468#define PY_ARRAY_UNIQUE_SYMBOL API_YEAH
    6569//#define NO_IMPORT_ARRAY
    66 #include "Numeric/arrayobject.h"
     70#include "numpy/arrayobject.h"
    6771#include <sys/types.h>
    6872
    … …  
    119123    return NULL;
    120124  }
     125
     126  // check that numpy array objects arrays are C contiguous memory
     127  CHECK_C_CONTIG(pointlist);
     128  CHECK_C_CONTIG(seglist);
     129  CHECK_C_CONTIG(holelist);
     130  CHECK_C_CONTIG(regionlist);
     131  CHECK_C_CONTIG(pointattributelist);
     132  CHECK_C_CONTIG(segmarkerlist);
    121133 
    122134  /* Initialize  points */
    … …  
    245257     abs quantity_ext.c compute_gradients
    246258     
    247   PyArray_FromDims allolws you to create a Numeric array with unitialized data.
     259  PyArray_FromDims allolws you to create a numeric array with unitialized data.
    248260   The first argument is the size of the second argument (
    249261   the dimensions array).
    … …  
    258270  dimensions[0] = out.numberoftriangles;
    259271  dimensions[1] = 3;   
    260   gentrianglelist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     272  gentrianglelist = (PyArrayObject *) anuga_FromDimsAndData(2,
    261273                                            dimensions,
    262274                                            PyArray_INT,
    … …  
    266278  dimensions[0] = out.numberofpoints;
    267279  dimensions[1] = 2;   
    268   genpointlist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     280  genpointlist = (PyArrayObject *) anuga_FromDimsAndData(2,
    269281                                         dimensions,
    270282                                         PyArray_DOUBLE,
    … …  
    274286  /* Add point marker list */
    275287  dimensions[0] = out.numberofpoints;
    276   genpointmarkerlist = (PyArrayObject *) PyArray_FromDimsAndData(1,
     288  genpointmarkerlist = (PyArrayObject *) anuga_FromDimsAndData(1,
    277289                                         dimensions,
    278290                                         PyArray_INT,
    … …  
    282294  dimensions[0] = out.numberofpoints;
    283295  dimensions[1] = out.numberofpointattributes;   
    284   genpointattributelist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     296  genpointattributelist = (PyArrayObject *) anuga_FromDimsAndData(2,
    285297                                          dimensions,
    286298                                          PyArray_DOUBLE,
    … …  
    292304  dimensions[0] = out.numberoftriangles;
    293305  dimensions[1] = out.numberoftriangleattributes;   
    294   gentriangleattributelist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     306  gentriangleattributelist = (PyArrayObject *) anuga_FromDimsAndData(2,
    295307                                           dimensions,
    296308                                           PyArray_DOUBLE,
    … …  
    300312  dimensions[0] = out.numberofsegments;
    301313  dimensions[1] = 2;   
    302   gensegmentlist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     314  gensegmentlist = (PyArrayObject *) anuga_FromDimsAndData(2,
    303315                                                    dimensions,
    304316                                                    PyArray_INT,
    … …  
    308320  /* Add segment marker list */
    309321  dimensions[0] = out.numberofsegments;
    310   gensegmentmarkerlist = (PyArrayObject *) PyArray_FromDimsAndData(1,
     322  gensegmentmarkerlist = (PyArrayObject *) anuga_FromDimsAndData(1,
    311323                                            dimensions,
    312324                                            PyArray_INT,
    … …  
    317329    dimensions[0] = out.numberoftriangles;
    318330    dimensions[1] = 3;   
    319     genneighborlist = (PyArrayObject *) PyArray_FromDimsAndData(2,
     331    genneighborlist = (PyArrayObject *) anuga_FromDimsAndData(2,
    320332                                                 dimensions,
    321333                                                 PyArray_INT,
    … …  
    324336    dimensions[0] = 0;
    325337    dimensions[1] = 0;   
    326     genneighborlist = (PyArrayObject *) PyArray_FromDims(2,
    327                                                         dimensions,
    328                                                         PyArray_INT);
     338    genneighborlist = (PyArrayObject *) anuga_FromDims(2,
     339                                                      dimensions,
     340                                                      PyArray_INT);
    329341  }
    330342 
    … …  
    351363 
    352364 
    353   /* These memory blocks are passed into Numeric arrays
     365  /* These memory blocks are passed into numeric arrays
    354366   so don't free them  */
    355367  /*

  • anuga_core/source/anuga/mesh_engine/test_all.py

    r4898 r7276  
    7676    return unittest.TestSuite(map(load, modules))
    7777
     78
    7879if __name__ == '__main__':   
    7980    suite = regressionTest()

  • anuga_core/source/anuga/mesh_engine/test_generate_mesh.py

    r6174 r7276  
    1212from anuga.mesh_engine.mesh_engine import generate_mesh
    1313
    14 import Numeric as num
     14import numpy as num
    1515
    1616from anuga.utilities.numerical_tools import ensure_numeric
    … …  
    4343                              pointattlist,segattlist, mode, points)
    4444
    45         correct = num.array([(1, 0, 2), (2, 3, 1)], num.Int)      #array default#
     45        correct = num.array([(1, 0, 2), (2, 3, 1)])
    4646        self.failUnless(num.alltrue(data['generatedtrianglelist'].flat == \
    4747                                    correct.flat),
    4848                        'trianglelist is wrong!')
    49         correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)], num.Int)      #array default#
     49        correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)])
    5050        self.failUnless(num.alltrue(data['generatedsegmentlist'].flat == \
    5151                                    correct.flat),
    … …  
    7474        data = generate_mesh(points,seglist,holelist,regionlist,
    7575                              pointattlist,segattlist, mode, points)
    76         correct = num.array([(1, 0, 2), (2, 3, 1)], num.Int)      #array default#
     76        correct = num.array([(1, 0, 2), (2, 3, 1)])
    7777        self.failUnless(num.alltrue(data['generatedtrianglelist'].flat == \
    7878                                    correct.flat),
    7979                        'trianglelist is wrong!')
    80         correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)], num.Int)      #array default#
     80        correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)])
    8181        self.failUnless(num.alltrue(data['generatedsegmentlist'].flat == \
    8282                                    correct.flat),
    … …  
    154154                              pointattlist,segattlist, mode, points)
    155155
    156         correct = num.array([(1, 0, 2), (2, 3, 1)], num.Int)      #array default#
     156        correct = num.array([(1, 0, 2), (2, 3, 1)])
    157157        self.failUnless(num.alltrue(data['generatedtrianglelist'].flat == \
    158158                                    correct.flat),
    159159                        'trianglelist is wrong!')
    160         correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)], num.Int)      #array default#
     160        correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)])
    161161        self.failUnless(num.alltrue(data['generatedsegmentlist'].flat == \
    162162                                    correct.flat),
    … …  
    170170       
    171171        self.failUnless(num.alltrue(data['generatedsegmentmarkerlist'] == \
    172                                     num.array([1,2,3,4], num.Int)),      #array default#
     172                                    num.array([1,2,3,4])),
    173173                        'Failed!')
    174174       
    … …  
    388388
    389389     
    390         correct = num.array([(1, 0, 2), (2, 3, 1)], num.Int)      #array default#
     390        correct = num.array([(1, 0, 2), (2, 3, 1)])
    391391        self.failUnless(num.alltrue(data['generatedtrianglelist'].flat == \
    392392                                    correct.flat),
    393393                        'trianglelist is wrong!')
    394         correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)], num.Int)      #array default#
     394        correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)])
    395395        self.failUnless(num.alltrue(data['generatedsegmentlist'].flat == \
    396396                                    correct.flat),
    … …  
    407407                                     correct.flat),
    408408                        'Failed')
    409         correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)], num.Int)      #array default#
     409        correct = num.array([(0, 1), (1, 3), (3, 2), (2, 0)])
    410410        self.failUnless(num.alltrue(data['generatedsegmentlist'].flat == \
    411411                                    correct.flat),
    412412                        'Failed!')
    413413       
    414         correct = num.array(segattlist, num.Int)      #array default#
     414        correct = num.array(segattlist, num.int)
    415415        self.failUnless(num.allclose(data['generatedsegmentmarkerlist'].flat,
    416416                                     correct.flat),
    … …  
    418418       
    419419        # I copied these answers from the output, so bad test..
    420         correct = num.array([(-1, 1, -1), (-1, 0, -1)], num.Int)      #array default#
     420        correct = num.array([(-1, 1, -1), (-1, 0, -1)])
    421421        self.failUnless(num.alltrue(data['generatedtriangleneighborlist'].flat == \
    422422                                    correct.flat),
    … …  
    463463                                     correct.flat),
    464464                        'Failed')
    465      
     465   
     466
    466467if __name__ == "__main__":
    467 
    468468    suite = unittest.makeSuite(triangTestCase,'test')
    469     #suite = unittest.makeSuite(triangTestCase,'testrectangleIIb')
    470     #suite = unittest.makeSuite(triangTestCase,'testsegmarker')
    471     #suite = unittest.makeSuite(triangTestCase,'testrectangle_regionsII')
    472469    runner = unittest.TextTestRunner()  #verbosity=2)
    473470    runner.run(suite)
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