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Commit 2b0d906a authored by Mads M. Pedersen's avatar Mads M. Pedersen
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bugfix in gtsdf dataset

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wetb/gtsdf/__init__.py
+ 5
− 2
View file @ 2b0d906a
......@@ -44,11 +44,14 @@ class Dataset(object):
self.time, self.data, self.info = load(filename)
def __call__(self, id):
if isinstance(id, str):
return self((['Time'] + self.info['attribute_names']).index(id) + 1)
if id=="Time":
return self.time
else:
return self(self.info['attribute_names'].index(id) + 2)
if id == 1:
return self.time
else:
return self.data[:, id - 1]
return self.data[:, id - 2]
def __getattribute__(self, name):
try:
......
wetb/gtsdf/tests/test_gtsdf.py
+ 3
− 2
View file @ 2b0d906a
......@@ -246,13 +246,14 @@ class Test_gsdf(unittest.TestCase):
def test_gtsdf_dataset(self):
ds = gtsdf.Dataset(tfp+'test.hdf5')
self.assertEqual(ds.data.shape, (2440,49))
self.assertEqual(ds('Time')[1], 0.05)
self.assertEqual(ds.Time[1], 0.05)
self.assertRaisesRegex(AttributeError, "'Dataset' object has no attribute 'Time1'", lambda : ds.Time1)
self.assertEqual(ds(2)[1], 11.986652374267578)
self.assertEqual(ds(2)[1], 12.04148006439209)
n = ds.info['attribute_names'][2]
self.assertEqual(n, "WSP gl. coo.,Vy")
self.assertEqual(ds(n)[1], 11.986652374267578)
self.assertEqual(ds(n)[1], 12.04148006439209)
......
wetb/utils/cython_compile/__init__.py deleted 100644 → 0
+ 0
− 11
View file @ 568ce00e
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
d = None;d = dir()
from .cython_compile import cython_compile, cython_import, cython_compile_autodeclare, is_compiled
__all__ = [m for m in set(dir()) - set(d)]
\ No newline at end of file
wetb/utils/cython_compile/cython_compile.py deleted 100644 → 0
+ 0
− 393
View file @ 568ce00e
'''
Created on 10/07/2013
@author: Mads M. Pedersen (mmpe@dtu.dk)
Wrapper functions and decorators for compiling functions using Cython
'''
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import dict
from io import open
from builtins import zip
from builtins import str
from future import standard_library
standard_library.install_aliases()
import inspect
import os
import re
import shutil
import subprocess
import sys
import numpy as np
import warnings
import imp
def wrap(f, autodeclare, *args, **kwargs):
"""
Wrapper function returned by the cython_compile and cython_compile_autodeclare decorators
:param f: Function to compile
:type f: function
:param py2pyx_func: py2pyx or py2pyx_autodeclare
:type py2pyx_func: function
"""
# Generate name: "c:\documents\project\mymodule.py" -> mymodule_myfunction
# When called from ipython notebooks, filename is an object e.g: "<ipython-input-12-e897f9fefc0c>"
# therefore <,>,- is removed to make it a legal python module name
name = os.path.relpath(inspect.getabsfile(f), str(os.getcwd())).replace(".py", "")
name = name.replace("<", "").replace(">", "").replace("-", "")
name = "%s_%s" % (name, f.__name__)
if name.startswith(".."):
rel_dir = os.path.dirname(name) + os.path.sep
sys.path.append(rel_dir)
name = name[len(rel_dir):]
pass
module_name = name.replace(os.path.sep, ".")
# import compiled module_name if exists, otherwise compile and import
try:
cmodule = __import__(module_name, fromlist="*")
if cmodule.__name__ != module_name or not hasattr(cmodule, f.__name__):
raise ImportError()
except ImportError:
# Generate pyrex code lines
if autodeclare:
pyx_lines = py2pyx_autodeclare(f, args, kwargs.copy())
else:
# source lines except '@cython_compile'
source_lines = inspect.getsourcelines(f)[0][1:]
indent = source_lines[0].index("def")
pyx_lines = py2pyx([l[indent:] for l in source_lines])
# Write pyrex code lines to .pyx file
pyx_filename = name.replace("\\", "/") + ".pyx"
with open(pyx_filename, 'w', encoding='utf-8') as fid:
fid.writelines(pyx_lines)
# compile, import compiled module_name and delete temporary files
cmodule = compile_and_cleanup(module_name, pyx_filename, module_name)
try:
cf = getattr(cmodule, f.__name__)
if kwargs == {}:
return cf(*args)
else:
return cf(*args, **kwargs)
except AttributeError:
warnings.warn(
"Compilation or import of %s failed. Python function used instead" %
f)
return f(*args, **kwargs)
def cython_compile(f):
"""Decorator for compilation, import and execution of the function, f.
Variables can be declared using Pure or cdef syntax, see module description
Example:
@cython_compile
def my_func(p):
pass
"""
w = lambda *args, **kwargs: wrap(f, False, *args, **kwargs)
w.__name__ = f.__name__
return w
def cython_compile_autodeclare(f):
"""Decorator for autodeclaring, compilation, import and execution of the function, f.
Declared variables using cdef syntax overrides autodeclaration, see module description
Example:
@cython_compile_autocompile
def my_func(p):
pass
"""
w = lambda *args, **kwargs: wrap(f, True, *args, **kwargs)
w.__name__ = f.__name__
return w
def cython_import(import_module_name, compiler=None):
"""Compiles and imports a module. Use it similar to the normal import
Example (import my_func from my_module):
from wetb.utils.cython_compile import cython_import
cython_import('my_module')
import my_module # import must be after cython_import statement
my_module.my_func()
"""
module_name = import_module_name.split(".")[-1]
globals()[module_name] = __import__(import_module_name, fromlist=module_name)
pyd_module = eval(module_name)
if not is_compiled(pyd_module):
# Read py-module
file_name = import_module_name.replace(".", "/") + ".py"
for p in ["."] + sys.path:
if os.path.isfile(os.path.join(p, file_name)):
file_path = os.path.join(p, file_name).replace("\\", "/")
break
else:
raise IOError("Module %s cannot be found" % file_name)
fid = open(file_path)
pylines = fid.readlines()
fid.close()
# write pyrex file
pyx_filename = file_path.replace('.py', '.pyx')
fid = open(pyx_filename, 'w')
pyxlines = py2pyx(pylines)
fid.writelines(pyxlines)
fid.close()
# compile, import compiled module and delete temporary files
module_relname = eval(module_name).__package__ + "." + module_name #"os.path.relpath(eval(module_name).__file__, str(os.getcwd())).replace(os.path.sep, ".")[:-3]
return compile_and_cleanup(import_module_name, pyx_filename, module_relname, compiler)
return eval(module_name)
def compile_and_cleanup(module, pyx_filename, module_relname, compiler=None):
"""compile, import compiled module and delete temporary files"""
# Generate setup.py script
fid = open('setup.py', 'w')
setup_str = """from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import numpy
ext_modules = [Extension("%s", ["%s"], include_dirs = [numpy.get_include()])]
setup(
name = 'name',
cmdclass = {'build_ext': build_ext},
ext_modules = ext_modules
)""" % (module_relname, pyx_filename)
fid.write(setup_str)
fid.close()
if hasattr(sys, 'frozen'):
raise Exception ("Trying to compile %s in frozen application" % str(module))
# create compile command
import platform
if compiler is not None:
compiler_str = "--compiler=%s" % compiler
elif platform.architecture()[0] == "32bit" and os.name == 'nt' and "mingw" in os.environ['path'].lower():
compiler_str = "--compiler=mingw32"
else:
compiler_str = ""
bin_python = sys.executable
cmd = "%s setup.py build_ext --inplace %s" % (bin_python, compiler_str)
# compile
print ("compiling %s: %s" % (module, cmd))
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
(out, err) = proc.communicate()
# Reload and check that module is compiled
try:
try:
del sys.modules[module]
except KeyError:
pass
cmodule = __import__(module, fromlist=module.split(".")[-1])
imp.reload(cmodule)
except ImportError:
cmodule = None
if cmodule is None or is_compiled(cmodule) == False:
line = '\n' + '=' * 79 + '\n'
sys.stderr.write("%s was not compiled correctly. It may result in slower execution" % module)
sys.stderr.write('%sstdout:\n%s' % (line, out.decode()))
sys.stderr.write('%sstderr:%s%s' % (line, line, err))
else:
print ("Compiling succeeded")
for f in ['setup.py', pyx_filename, pyx_filename.replace(".pyx", '.c')]:
if os.path.isfile(f):
os.remove(f)
# Clean up. Remove temporary files and folders
if os.path.isdir("build"):
try:
shutil.rmtree("build")
except:
pass
return cmodule
def py2pyx_autodeclare(f, args, kwargs):
"""Generate pyrex code of function f and its input arguments
This function invokes py2pyx and extends with autodeclarations:
- arguments: input arguments are declared based their values in args and kwargs
- cdef: Variables declared by cdef, overrides autodeclaration, e.g:
"def func(a): #cpdef func(int a):" -> "cpdef func(int a):" (independent of type of a)
"#cdef int a" - "cdef int a" (independent of type of a)
- assignment: Variables assigned in function, e.g.
"a = xxx"
are declared based on the type of eval(xxx)
- in: variables returned by iterators, e.g:
"for a in range(5)",
"for a,b in [(1,.2)]:"
are declared base on the type of the first element in eval(iterator), e.g. "type(eval(range(5)[0]))"
"""
arg_names, _, _, defaults = inspect.getargspec(f)
# update kwargs with defaults
if defaults:
for k, v in zip(arg_names[::-1], defaults[::-1]):
if k not in kwargs:
kwargs[k] = v
kwargs.update(dict(zip(arg_names, args)))
# get pyx code lines using py2pyx
lines = inspect.getsourcelines(f)[0]
if lines[0].strip() == "@cython_compile_autodeclare":
lines = lines[1:]
lines = py2pyx(lines)
# prepare regular expressions
var_name = "(?:_*[a-zA-Z][a-zA-Z0-9_]*)" # optional "_" + one alpha + [0..n] x alphanum. "?:" = no group
reg_args = re.compile("[ \t]*def +(?:%s) *\(([^:]*)\) *:" % (var_name))
reg_import = re.compile("[ \t]*c?import *(%s)(?: +as +(%s))?" % (var_name, var_name))
reg_cdef = re.compile("[ \t]*cdef +(?:(?:signed|unsigned|int|long|float|double|np\.ndarray\[.*\]) *)*(%s)" % var_name)
reg_assign = re.compile('[ \t]*(%s) *=(.*)' % var_name)
reg_in = re.compile('[ \t]*for +(%s(?:, *%s)*) +in +(.*):' % (var_name, var_name))
def declare_str(var_name, var_value):
"""Generate declaration string '<type(var_value)> <var_name>' e.g:
declare_str('a',1) -> "long a"
"""
if isinstance(var_value, (int)):
return "long long %s" % var_name
if isinstance(var_value, float):
return "double %s" % var_name
elif isinstance(var_value, np.ndarray):
return "np.ndarray[np.%s_t,ndim=%d] %s" % (var_value.dtype, len(var_value.shape), var_name)
else:
raise NotImplementedError(type(var_value))
defs = {} # dict for known local variables
def_line = None # line nr of "def func():". Autodeclaration of local field inserted below this line
for i, line in enumerate(lines):
if def_line is None and 'def' in line:
# first line containing "def" = function declaration line
def_line = i
match = reg_args.match(line)
if match is not None:
args = match.group(1).strip() # line=" def func(xxx):#comment" -> args='xxx'
arg_strs = []
if args != "":
for arg in args.split(','):
arg_name = arg.split('=')[0].strip()
arg_value = kwargs[arg_name]
try:
arg_strs.append(arg.strip().replace(arg_name, declare_str(arg_name, arg_value), 1))
except NotImplementedError:
arg_strs.append(arg)
# replace function declaration line
lines[i] = '%scpdef %s(%s):\n' % (" " * line.index('def'), f.__name__, ", ".join(arg_strs))
else:
#Import: import x as y
match = reg_import.match(line)
if match is not None:
# add imported moduled to kwargs -> enable evaluation of variables
import_module = match.group(1)
if match.group(2) is None:
kwargs[import_module] = __import__(import_module)
else:
# import xxx as y
kwargs[match.group(2)] = __import__(import_module)
continue
#Cdef: cdef int x
match = reg_cdef.match(line)
if match is not None:
# line contains a 'cdef' declaration.
# Add to defs to avoid redeclaration
var_name = match.group(1)
if var_name not in defs:
defs[var_name] = None
continue
#Assignment: x = y
match = reg_assign.match(line)
if match is not None:
# line contains an assignment, e.g. a = xxx.
# Try to evaluate xxx and declare a as type of eval(xxx)
try:
var_name = match.group(1)
if var_name not in defs:
var_value = eval(match.group(2), globals(), kwargs)
defs[var_name] = declare_str(
var_name.strip(), var_value)
kwargs[var_name] = var_value
except NotImplementedError:
pass
continue
#In: For x in y
match = reg_in.match(line)
if match is not None:
# line contains 'for xxx in yyy:'.
# Try to evaluate yyy and declare xxx as type of first element
# of eval(yyy)
var_names = [v.strip() for v in match.group(1).split(",")]
var_values = eval(match.group(2), globals(), kwargs)[0]
if not isinstance(var_values, (list, tuple)):
var_values = (var_values,)
for var_name, var_value in zip(var_names, var_values):
try:
if var_name not in defs:
defs[var_name] = declare_str(var_name, var_value)
kwargs[var_name] = var_value
except NotImplementedError:
pass
indent = lines[def_line + 1].replace(lines[def_line + 1].lstrip(), "")
# Insert declaration of local fields ordered by name just below function
# declaration
for key in sorted(defs.keys(), reverse=True):
if defs[key] is not None:
lines.insert(def_line + 1, "%scdef %s\n" % (indent, defs[key]))
return lines
def py2pyx(pylines):
"""Generate pyrex code lines from python code lines
- Adds import of cython and numpy
- searches every line for "#c". If found text before "#c" is replaced with text after "#c", e.g:
"def func(a): #cpdef func(int a):" -> "cpdef func(int a):
"#cdef int b" -> "cdef int b"
"""
pyxlines = ['import cython\n', 'import numpy as np\n', 'cimport numpy as np\n']
for l in pylines:
if "#c" in l:
indent = l[:len(l) - len(l.lstrip())]
cdef = l[l.index("#c") + 1:]
l = indent + cdef
if "__future__" in l:
#pyxlines.insert(0, l) # from __future__ import ... must be first
pass
else:
pyxlines.append(l)
return pyxlines
def is_compiled(module):
return module.__file__.lower()[-4:] == ".pyd" or module.__file__.lower()[-3:] == ".so"
wetb/utils/cython_compile/examples/__init__.py deleted 100644 → 0
+ 0
− 0
View file @ 568ce00e
wetb/utils/cython_compile/examples/cycheck.py deleted 100644 → 0
+ 0
− 41
View file @ 568ce00e
'''
Created on 29/03/2013
@author: Mads
'''
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from builtins import range
from builtins import int
from future import standard_library
standard_library.install_aliases()
import cython
import math
def cycheck(p):
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
@cython.ccall
@cython.locals(y=cython.int, p=cython.ulonglong)
def cycheck_pure(p):
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
def cycheck_cdef(p): #cpdef cycheck_cdef(unsigned long long p):
#cdef int y
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
wetb/utils/cython_compile/examples/examples.py deleted 100644 → 0
+ 0
− 62
View file @ 568ce00e
'''
Created on 11/07/2013
@author: Mads M. Pedersen (mmpe@dtu.dk)
'''
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import range
from builtins import int
from future import standard_library
standard_library.install_aliases()
import math
from wetb.utils.cython_compile.cython_compile import cython_compile, \
cython_compile_autodeclare, cython_import
from wetb.utils.cython_compile.examples import cycheck
def pycheck(p):
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
@cython_compile
def cycheck_compile(p):
import math
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
@cython_compile_autodeclare
def cycheck_compile_autodeclare(p):
import math
for i in range(10):
for y in range(2, int(math.sqrt(p)) + 1):
if p % y == 0:
return False
return True
if __name__ == "__main__":
p = 17
print (pycheck(p))
cython_import('cycheck')
print (cycheck.cycheck(p))
print (cycheck.cycheck_pure(p))
print (cycheck.cycheck_cdef(p))
print (cycheck_compile(p))
print (cycheck_compile_autodeclare(p))
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