def _get_data(gwydf, xres, yres):
"""Get data array from <GwyDataField*> object
Args:
gwydf (GwyDataField*):
GwyDataField object from Libgwyfile
xres (int): Horizontal dimension of the data field in pixels
yres (int): Vertical dimension of the data field in pixels
Returns:
data (2D numpy array, float64): data from the data field
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
data = ffi.new("double[]", xres * yres)
datap = ffi.new("double**", data)
if lib.gwyfile_object_datafield_get(gwydf, errorp,
ffi.new("char[]", b'data'), datap,
ffi.NULL):
data_buf = ffi.buffer(datap[0], xres * yres * ffi.sizeof(data))
data_array = np.frombuffer(data_buf,
dtype=np.float64,
count=xres * yres).reshape((xres, yres))
return data_array
else:
raise GwyfileErrorCMsg(errorp[0].message)
def _side_effect(self, *args):
"""
Check args of gwyfile_object_graphmodel_get func
and write self.curves_array in 'curves' field
"""
# first arg is GwyDatafield returned by get_gwyitem_object
self.assertEqual(args[0], self.gwygraphmodel)
# second arg is GwyfileError**
assert ffi.typeof(args[1]) == ffi.typeof(ffi.new("GwyfileError**"))
# last arg in Null
self.assertEqual(args[-1], ffi.NULL)
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['curves'][0] = self.curves_array
# C func returns true if the graphmodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _get_curves(gwygraphmodel, ncurves):
"""Get list of GwyGraphCurveModel object pointers
Args:
gwygraphmodel (GwyGraphModel*):
GwyGraphModel object from Libgwyfile C library
ncurves (int):
number of curves in the GwyGraphModel object
Returns:
curves (list):
list of GwyGraphCurveModel* Libgwyfile objects
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
curves_arrayp = ffi.new("GwyfileObject***")
curves = []
if lib.gwyfile_object_graphmodel_get(gwygraphmodel, errorp,
ffi.new("char[]", b"curves"),
curves_arrayp, ffi.NULL):
curves_array = curves_arrayp[0]
curves = [curves_array[curve_id] for curve_id in range(ncurves)]
return curves
else:
raise GwyfileErrorCMsg(errorp[0].message)
def _get_selection_points(cls, gwysel, nsel):
"""Get all points of selection from the gwysel object
Args:
gwysel (GwyfileObject*):
GwySelection object from Libgwyfile
e.g. GwySelectionPoint object for point selection
nsel (int):
number of selections of this type in gwysel
Returns:
[(x1, y1), ..., (xN, yN)]: list of tuples with point coordinates
or None if there are no selections
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
if nsel == 0:
return None
else:
data = ffi.new("double[]", 2 * nsel * cls._npoints)
datap = ffi.new("double**", data)
if cls._get_sel_func(gwysel, errorp, ffi.new("char[]", b'data'), datap,
ffi.NULL):
data = datap[0]
points = [(data[i * 2], data[i * 2 + 1])
for i in range(nsel * cls._npoints)]
else:
raise GwyfileErrorCMsg(errorp[0].message)
return points
def write_gwycontainer_to_gwyfile(gwycontainer, filename):
"""Write gwycontainer to file.
The file will be overwritten if it exists
Args:
gwycontainer (<GwyfileObject*>)
filename (string): name of file
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
if not lib.gwyfile_write_file(
gwycontainer, ffi.new("char[]", filename.encode('utf-8')), errorp):
raise GwyfileErrorCMsg(errorp[0].message)
def _test_pos_args_side_effect(self, *args):
# first arg is GwyfileSelectionPoint object
self.assertEqual(args[0], self.gwysel)
# second arg is GwyfileError**
self.assertEqual(ffi.typeof(args[1]),
ffi.typeof(ffi.new("GwyfileError**")))
# last arg in Null
self.assertEqual(args[-1], ffi.NULL)
# Function should return True if object looks acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _getting_description_of_curve(self, *args):
"""
Write self.description in 'description' field and return True
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['description'][0] = ffi.new("char[]",
self.description.encode('utf-8'))
# C func returns true if the graphcurvemodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def setUp(self):
self.cgwydf = Mock()
self.mock_gwydf = Mock(spec=GwyDataField)
self.mock_gwydf._get_data = GwyDataField._get_data
patcher_lib = patch('pygwyfile.gwydatafield.lib', autospec=True)
self.addCleanup(patcher_lib.stop)
self.mock_lib = patcher_lib.start()
self.falsep = ffi.new("bool*", False)
self.truep = ffi.new("bool*", True)
self.errorp = ffi.new("GwyfileError**")
self.error_msg = "Test error message"
self.xres = 256
self.yres = 256
self.data = np.random.rand(self.xres, self.yres)
def _y_unit_is_not_empty(self, *args):
"""
Write "m" C string to 'y_unit' field
"""
y_unit = ffi.new("char[]", b"m")
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['y_unit'][0] = y_unit
# C func returns true if the graphmodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def setUp(self):
self.gwysel = Mock()
self.nsel = 2
self.points = [(0., 0.), (1., 1.)]
self.cpoints = ffi.new("double[]", [0., 0., 1., 1.])
patcher = patch.object(GwySelection, '_get_sel_func')
self.get_sel_func = patcher.start()
self.addCleanup(patcher.stop)
def _side_effect_non_zero_channels(self, c_gwyfile, nchannelsp):
"""
Returns 3 channels with ids = 0, 1 and 2
"""
nchannelsp[0] = 3
ids = ffi.new("int[]", [0, 1, 2])
return ids
def _side_effect_non_zero_graphs(self, c_gwyfile, ngraphsp):
"""
Returns 2 graphs with ids = 1 and 2
"""
ngraphsp[0] = 2
ids = ffi.new("int[]", [1, 2])
return ids
def setUp(self):
self.ncurves = 3 # number of curves in graphmodel object
self.curves_array = ffi.new("GwyfileObject*[]", self.ncurves)
self.gwygraphmodel = Mock()
patcher_lib = patch('pygwyfile.gwygraph.lib', autospec=True)
self.addCleanup(patcher_lib.stop)
self.mock_lib = patcher_lib.start()
def _positional_args_side_effect(self, *args):
"""
Check positional args in gwyfile_object_graphcurvemodel_get call
"""
# first arg is GwyGraphCurveModel
self.assertEqual(args[0], self.gwycurve)
# second arg is GwyfileError**
assert ffi.typeof(args[1]) == ffi.typeof(ffi.new("GwyfileError**"))
# last arg in Null
self.assertEqual(args[-1], ffi.NULL)
# C func returns true if the graphcurvemodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _cdata(self):
""" Representation of pointer selections list as C array
"""
if self.data:
flat_data_list = [val for point in self.data for val in point]
cdata = ffi.new("double[]", flat_data_list)
return cdata
else:
return None
def _y_max_set_is_false(self, *args):
"""
Write False in 'y_max_set' field and 0. in 'y_max' field
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
truep = ffi.new("bool*", True)
falsep = ffi.new("bool*", False)
arg_dict['y_max_set'][0] = falsep[0]
arg_dict['y_max'][0] = 0.
# C func returns true if the graphmodel object loock acceptable
return truep[0]
def test_raise_exception_if_graphmodel_object_looks_unacceptable(self):
"""
Raise GwyfileErrorCMsg if gwyfile_object_graphmodel_get returns False
"""
falsep = ffi.new("bool*", False)
self.mock_lib.gwyfile_object_graphmodel_get.return_value = falsep[0]
self.assertRaises(GwyfileErrorCMsg, GwyGraphModel._get_curves,
self.gwygraphmodel, self.ncurves)
def new_gwycontainer():
""" Create new empty GwyContainer
Returns:
gwycontainer (<cdata GwyfileObject*>):
empty Gwyddion Container
"""
gwycontainer = lib.gwyfile_object_new(ffi.new("char[]", b"GwyContainer"),
ffi.NULL)
return gwycontainer
def test_raise_exception_in_get_selection_points(self):
"""Raise GwyfileErrorCMsg in GwySelection._get_selection_points
Raise GwyfileErrorCMsg in GwySelection._get_selection_points
if get_sel_func returns False
"""
falsep = ffi.new("bool*", False)
self.get_sel_func.return_value = falsep[0]
self.assertRaises(GwyfileErrorCMsg, GwySelection._get_selection_points,
self.gwysel, self.nsel)
def test_raise_exception_if_graphcurvemodel_looks_unacceptable(self):
"""
Raise GwyfileErrorCMsg if GwyGraphCurveModel looks unacceptable
"""
falsep = ffi.new("bool*", False)
self.mock_lib.gwyfile_object_graphcurvemodel_get.return_value = (
falsep[0])
self.assertRaises(GwyfileErrorCMsg, GwyGraphCurve._get_data,
self.gwycurve, self.npoints)
def _label_has_frame(self, *args):
"""
Write self.label_has_frame in 'label.has_frame' field
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
truep = ffi.new("bool*", True)
falsep = ffi.new("bool*", False)
if self.label_has_frame:
arg_dict['label.has_frame'][0] = truep[0]
else:
arg_dict['label.has_frame'][0] = falsep[0]
# C func returns true if the graphmodel object loock acceptable
return truep[0]
def _test_returned_value(self, *args):
"""Write self.nsel in 'nsel' and return True
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['nsel'][0] = self.nsel
# Function should return True if object looks acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _get_points_side_effect(self, *args):
""" Write self.cpoints in 'data' field and return True
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['data'][0] = self.cpoints
# Function should return True if object looks acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _side_effect_return_metadata(self, *args):
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
for key in arg_dict:
if key not in ['si_unit_xy', 'si_unit_z']:
arg_dict[key][0] = self.test_metadata_dict[key]
else:
metadata_value = self.test_metadata_dict[key].encode('utf-8')
metadata_c_str = ffi.new("char[]", metadata_value)
arg_dict[key][0] = metadata_c_str
return self.truep[0]
def _label_position(self, *args):
"""
Write self.label_position in 'label.position' field
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['label.position'][0] = self.label_position
# C func returns true if the graphmodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _get_selection_nsel(cls, gwysel):
"""Get number of selections from the object
Args:
gwysel (GwyfileObject*):
GwySelection object from Libgwyfile
e.g. GwySelectionPoint object for point selection
Returns:
nsel (int):
number of selections of this type in gwysel
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
nselp = ffi.new("int32_t*")
if cls._get_sel_func(gwysel, errorp, ffi.new("char[]", b'nsel'), nselp,
ffi.NULL):
nsel = nselp[0]
else:
raise GwyfileErrorCMsg(errorp[0].message)
return nsel
def from_gwy(filename):
"""Create Gwyfile instance from file
Args:
filename (string): filename including path
Returns:
Gwyfile:
instnce of Gwyfile class
"""
error = ffi.new("GwyfileError*")
errorp = ffi.new("GwyfileError**", error)
if not os.path.isfile(filename):
raise OSError("Cannot find file {}".format(filename))
c_gwyfile = lib.gwyfile_read_file(filename.encode('utf-8'), errorp)
if not c_gwyfile:
raise GwyfileErrorCMsg(errorp[0].message)
gwyfile = Gwyfile(c_gwyfile)
return gwyfile
def _get_number_of_curves(self, *args):
"""
Return 3 as a number of curves in graphmodel object
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['ncurves'][0] = 3
# C func returns true if the graphmodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _x_unit_is_empty(self, *args):
"""
Write NULL to x_unit field
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['x_unit'][0] = ffi.NULL
# C func returns true if the graphmodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
def _getting_line_size_side_effect(self, *args):
"""
Write self.line_size in 'line_size' field and return True
"""
# combine fields names and fields pointers in one dictionary
arg_keys = [ffi.string(key).decode('utf-8') for key in args[2:-1:2]]
arg_pointers = [pointer for pointer in args[3:-1:2]]
arg_dict = dict(zip(arg_keys, arg_pointers))
arg_dict['line_size'][0] = self.line_size
# C func returns true if the graphcurvemodel object loock acceptable
truep = ffi.new("bool*", True)
return truep[0]
