anuga 1.3.5__zip

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/__init__.py

@@ -0,0 +1,11 @@
+"""Make directory available as a Python package
+"""
+
+from numpy.testing import Tester
+test = Tester().test
+
+
+
+
+
+

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/add_csv_header.py

@@ -0,0 +1,136 @@
+#!/usr/bin/env python
+
+'''Routine to add a header to a CSV file.
+'''
+
+import os
+import tempfile
+
+
+def add_csv_header(file, header_list, be_green=False):
+    """Add a CSV header line to a text file.
+
+    file         Path to the file to add header to
+    header_list  A list of strings - the header to insert
+    be_green     If True, go easy on memory, but slower
+
+    Checks that the first line of the original file has the same number of
+    fields as the new header line.  Raises exception if thi is not true.
+
+    The 'be_green' option is not yet implemented.
+    """
+
+    # open the file to insert header into
+    try:
+        fd = open(file, 'r')
+    except IOError, e:
+        msg = "Can't open file '%s': %s" % (file, str(e))
+        raise Exception, msg
+    except:
+        msg = "Can't open file '%s'" % file
+        raise Exception, msg
+
+    # get a temporary file.
+    # must create in same directory as input file, as we rename it.
+    input_dir = os.path.dirname(file)
+    (tmp_f, tmp_filename) = tempfile.mkstemp(dir=input_dir)
+    tmp_fd = os.fdopen(tmp_f, 'w')
+
+    # check the header, create header _string.
+    if header_list is None or header_list is []:
+        msg = "add_csv_header: header_list can't be None or []"
+        raise Exception, msg
+
+    header_string = ','.join(header_list) + '\n'
+
+    # copy header to output file, then input file
+    tmp_fd.write(header_string)
+
+    if be_green:
+        first_line = True
+        for line in fd:
+            if first_line:
+                first_line = False
+                columns = line.strip().split(',')
+                if len(columns) != len(header_list):
+                    msg = ("add_csv_header: File %s has %d columns but header "
+                           "has %d columns" % (file, len(columns), len(header_list)))
+                    raise Exception, msg
+            tmp_fd.write(line)
+    else:
+        data = fd.readlines()
+        columns = data[0].strip().split(',')
+
+        if len(columns) != len(header_list):
+            msg = ("add_csv_header: File %s has %d columns but header "
+                   "has %d columns" % (file, len(columns), len(header_list)))
+            raise Exception, msg
+
+        data = ''.join(data)
+        tmp_fd.write(data)
+
+    # close and rename all files
+    tmp_fd.close()
+    fd.close()
+    os.rename(tmp_filename, file)
+
+
+if __name__ == '__main__':
+    import sys
+    import os
+
+    file_data = '1,2,3\n4,5,6\n7,8,9'
+    header = ['alpha', 'bravo', 'charlie']
+    filename = '/tmp/add_csv_header.csv'
+    filename2 = '/tmp/add_csv_header2.csv'
+
+######
+# Create file and test function.
+######
+
+    # create test file
+    fd = open(filename, 'w')
+    fd.write(file_data)
+    fd.close()
+
+    add_csv_header(filename, header)
+
+    # read test file
+    fd = open(filename, 'r')
+    data = fd.readlines()
+    fd.close
+
+    # check if data as expected
+    data = ''.join(data)
+    header_string = ','.join(header) + '\n'
+    expected = header_string + file_data
+
+    msg = 'Expected data:\n%s\ngot:\n%s' % (expected, data)
+    assert expected == data, msg
+
+######
+# Test the 'be_green' option.
+######
+
+    # create test file
+    fd = open(filename2, 'w')
+    fd.write(file_data)
+    fd.close()
+
+    add_csv_header(filename2, header, be_green=True)
+
+    # read test file
+    fd = open(filename2, 'r')
+    data = fd.readlines()
+    fd.close
+
+    # check if data as expected
+    data = ''.join(data)
+    header_string = ','.join(header) + '\n'
+    expected = header_string + file_data
+
+    msg = 'Expected data:\n%s\ngot:\n%s' % (expected, data)
+    assert expected == data, msg
+
+    os.remove(filename)
+    os.remove(filename2)

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/file_length.py

@@ -0,0 +1,14 @@
+"""Function to return the length of a file.
+
+Intended to be used for simplfying the creation of boundary_tags in
+run_model.py
+
+Input: filename
+Returns: number of lines in file
+"""
+def file_length(in_file):
+    fid = open(in_file)
+    data = fid.readlines()
+    fid.close()
+    return len(data)
+

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/maxasc.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+"""
+The MaxAsc() function.
+Takes 1 or more ASC files and generates an output ASC file with
+an element-wise maximum.
+"""
+
+import sys
+import re
+
+# if user does 'from ... import *' only give her/him MaxAsc
+__all__ = ['MaxAsc']
+
+HEADER_SIZE = 6
+
+# pattern string used to split multimax data
+SpacesPatternString = ' +'
+
+# generate 're' pattern for 'any number of spaces'
+SpacesPattern = re.compile(SpacesPatternString)
+
+
+def MaxAsc(out_file, in_files):
+    """
+    MaxAsc('output_filename', ['list', 'of', 'filenames'])
+    
+    The output file is an ASC file with each element being the maximum of
+    the corresponding element in all the input ASC files.  The output file
+    has the same shape as the input file(s).
+    """
+    
+    # get all file data into memory
+    file_data = []
+    for f in in_files:
+        fd = open(f, 'r')
+        data = fd.readlines()
+        file_data.append(data)
+        fd.close()
+
+    # check we have same number of lines in each file
+    num_lines = len(file_data[0])
+    for (i, d) in enumerate(file_data):
+        if len(d) != num_lines:
+            raise RuntimeError, \
+                  ("File %s has the wrong number of lines "
+                   "(%d, expected %d)." % (in_files[i], len(d), num_lines))
+    
+    # open the output file
+    out_fd = open(out_file, 'w')
+
+    # read header lines, check same, write out
+    for i in range(HEADER_SIZE):
+        line = file_data[0][i]
+        for (j, f) in enumerate(file_data):
+            d = f[i]
+            if d != line:
+                out_fd.close()
+                raise RuntimeError, \
+                      "File %s has the wrong header at line %d." % \
+                      (in_files[j], i)
+        out_fd.write(line)
+
+    # read data lines
+    for line_num in range(HEADER_SIZE, num_lines):
+        lines = []
+        col_file = ''
+        columns = None
+        for (i, f) in enumerate(file_data):
+            data = f[line_num]
+            if len(data) > 1:
+                data = data.strip()
+                data = SpacesPattern.split(data)
+                if columns:
+                    if columns != len(data):
+                        out_fd.close()
+                        raise RuntimeError, \
+                              ("File %s doesn't have same number of columns "
+                               "(%d) as file %s (%d), line %d!?" %
+                               (fd.name, len(data), col_file, columns, line_num))
+                else:
+                    col_file = in_files[i]
+                    columns = len(data)
+                fdata = [float(value) for value in data]
+                lines.append(fdata)
+        outline = ''
+        for i in range(columns):
+            maximum = lines[0][i]
+            for d in lines:
+                if maximum < d[i]:
+                    maximum = d[i]
+            outline += ' %10.4e ' % maximum
+        out_fd.write('%s\n' % outline)
+        
+    # close the output file
+    out_fd.close()

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/order_boundary.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+'''Routine to automatically order boundary points'''
+
+################################################################################
+# This routine is used to automatically order boundary points in a CSV file.
+#
+# usage: order_boundary(infile, outfile)
+#
+# where infile  is the string path of the input CSV file,
+#   and outfile is the string path of the output CSV file.
+#
+# The input file is expected to have the format:
+#        longitude,latitude,index
+#        150.0833,-37.5,2758
+#        150.1,-37.4667,2765
+#        150.1167,-37.3833,2769
+#        150.1333,-36.7167,2771
+#        150.1333,-36.7667,2774
+#        150.15,-36.5833,2777
+#        150.15,-36.6333,2780
+#        150.15,-36.6833,2783
+#        150.15,-36.8167,2787
+#
+# The first point in the ordered output file is assumed to be the first point in
+# the input file (ie, line 2).  The header line is preserved, as are all fields
+#following the first two fields in each data line.
+################################################################################
+
+import csv
+
+
+def order_boundary(infile, outfile):
+    """Order a CSV file of boundary points.
+
+    infile   path to input filep
+    outfile  path to output filep
+
+    Input file will have a header line that must be preserved.
+    File format is: (longitude, latitude, <other_fields>)
+    Fields after long+lat must be preserved.
+    """
+
+    def sort_points(unordered, ordered, id):
+        """Sort a list of point tuples.
+
+        unordered  unordered list of points.
+        ordered    return list of ordered points.
+        id         is index into 'unordered' of point to put into 'ordered'
+
+        This code:
+            . moves 'id' point from 'unordered' into 'ordered'
+            . finds 'id' of next point to be moved
+            . if more points, recurse
+        """
+
+        # move 'id' point from unordered to ordered, get x0, y0
+        ordered.append(unordered[id])
+        x0 = unordered[id][0]
+        y0 = unordered[id][1]
+        del unordered[id]
+
+        # find nearest point to 'id' point in 'unordered'
+        nearest = None
+        for i, p in enumerate(unordered):
+            x1 = p[0]
+            y1 = p[1]
+            # get square of distance between the 2 points
+            d2 = (x1-x0)*(x1-x0) + (y1-y0)*(y1-y0)
+            if nearest is None or d2 < nearest:
+                next = i
+                nearest = d2
+
+        # if there are more points in 'unordered', recurse
+        if nearest is not None:
+            sort_points(unordered, ordered, next)
+            
+        return ordered
+
+    # read file into list of tuples, convert first 2 fields to floats.
+    fd = open(infile, 'r')
+    data = []
+    for row in csv.reader(fd):
+        try:
+            row[0] = float(row[0])
+        except:
+            pass
+        try:
+            row[1] = float(row[1])
+        except:
+            pass
+        data.append(tuple(row))
+    fd.close()
+
+    # preserve header row
+    header = data[0]
+    del data[0]
+
+    # order the data
+    ordered_data = sort_points(data, [], 0)
+
+    # write ordered data to output file
+    fd = open(outfile, 'wb')
+    w = csv.writer(fd)
+    w.writerow(header)
+    
+    for d in ordered_data:
+        w.writerow(d)
+    fd.close()
+

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/setup.py

@@ -0,0 +1,22 @@
+from __future__ import division, print_function
+
+import os
+import sys
+
+from os.path import join
+
+def configuration(parent_package='',top_path=None):
+    
+    from numpy.distutils.misc_util import Configuration
+    from numpy.distutils.system_info import get_info
+    
+    config = Configuration('lib', parent_package, top_path)
+
+    config.add_data_dir('tests')
+
+    
+    return config
+    
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(configuration=configuration)

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/__init__.py

@@ -0,0 +1,8 @@
+"""Make directory available as a Python package
+"""
+
+pass
+
+
+
+

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/perthAll_stage_250m.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>perthAll_stage_250m.asc</filename>
+    <checksum>1646268307</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/perthAll_stage_250m_all.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>perthAll_stage_250m_all.asc</filename>
+    <checksum>4150847986</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/perthAll_stage_original.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>perthAll_stage_original.asc</filename>
+    <checksum>2381579737</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+  
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1.asc

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Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>test1.asc</filename>
+    <checksum>3809587973</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_bad_num_lines.asc

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Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_bad_num_lines.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>test1_bad_num_lines.asc</filename>
+    <checksum>3331055575</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_header_differs.asc

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Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_header_differs.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>test1_header_differs.asc</filename>
+    <checksum>506435569</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_wrong_num_columns.asc

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Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test1_wrong_num_columns.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>test1_wrong_num_columns.asc</filename>
+    <checksum>189975811</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test2.asc

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Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test2.expected.asc

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+nrows         11
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+yllcorner     6408555
+cellsize      250.000000
+NODATA_value  -9999
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+ -9999.0000 -9999.0000 0.6015 57.9600
+ -9999.0000 -9999.0000 0.6012 0.5870
+ -9990.0000 -9991.0000 -9992.0000 -9993.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000
+ 9998.0000 -9999.0000 -9999.0000 -9999.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000
+ -9999.0000 -9999.0000 -9999.0000 -9999.0000

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/lib/tests/test2.expected.lic

@@ -0,0 +1,17 @@
+<?xml version='1.0' encoding='iso-8859-1'?>
+<ga_license_file>
+  <metadata>
+    <author>Ross Wilson</author>
+  </metadata>
+  
+  <datafile>
+    <filename>test2.expected.asc</filename>
+    <checksum>2958591099</checksum>
+    <publishable>Yes</publishable>
+    <accountable>Ross Wilson</accountable>
+    <source>Generated by ANUGA development team</source>
+    <IP_owner>Geoscience Australia</IP_owner>
+    <IP_info>Test data file used by test_all.py</IP_info>    
+  </datafile>
+
+</ga_license_file>