def matrix4D_reader(wfile, header=False, delimiter=',', *args, **kwargs):
"""temporary wrapper for new readers, replace call to matrix4D_reader
with calls to read_data(wfile,reader=matrix4D_reader).
read csv data with parameters extracted from header as saved by 4D.
"""
from pySurf.readers.format_reader import csv4D_reader
#import pdb
#pdb.set_trace()
return read_data(wfile, csv4D_reader, delimiter=delimiter, *args, **kwargs)
def points_reader(wfile, *args, **kwargs):
"""temporary wrapper for points readers, read and register
points and convert to 2D data"""
from pySurf.readers.format_reader import points_reader
return read_data(wfile, points_reader, *args, **kwargs)
def fits_reader(wfile, *args, **kwargs):
"""temporary wrapper for new readers, replace call to fits_reader
with calls to read_data(wfile,reader=fits_reader)"""
from pySurf.readers.format_reader import fits_reader
return read_data(wfile, fits_reader, *args, **kwargs)
def matrixdat_reader(wfile, *args, **kwargs):
"""temporary wrapper for zygo metropro .dat binary files"""
from pySurf.readers.format_reader import datzygo_reader
return read_data(wfile, datzygo_reader, *args, **kwargs)
def matrixsur_reader(wfile, *args, **kwargs):
"""temporary wrapper for new readers, replace call to matrixsur_reader
with calls to read_data(wfile,reader=sur_reader)"""
from pySurf.readers.format_reader import sur_reader
return read_data(wfile, sur_reader, *args, **kwargs)
def matrix_reader(wfile, *args, **kwargs):
"""temporary wrapper for new readers, replace call to matrix4D_reader
with calls to read_data(wfile,reader=matrix4D_reader)"""
from pySurf.data2D import data_from_txt
return read_data(wfile, data_from_txt, *args, **kwargs)
def matrixZygo_reader(wfile, *args, **kwargs):
"""temporary wrapper for new readers, replace call to matrixZygo_reader
with calls to read_data(wfile,reader=csvZygo_reader)"""
from pySurf.readers.format_reader import csvZygo_reader
#pdb.set_trace()
return read_data(wfile, csvZygo_reader, *args, **kwargs)
def __init__(
self,
data=None,
x=None,
y=None,
file=None,
reader=None,
units=None,
name=None,
*args,
**kwargs
):
"""
A class for 2D data with coordinates and their analysis.
Can be initialized with data | data, x, y | file | file, x, y.
if x and y are coordinates if match number of elements,
or used as range if two element.
If provided together with file, they override x and y
read from file.
Function methods return a copy with new values and don't alter original
object. Reassign to variable to use as modifier:
e.g. a=a.level( ... )
Args:
data (2D array or string): 2D data or file name (suitable reader must
provided).
x, y (array): coordinates or ranges.
file (str): alternative way to provide a data file.
units (str array): 3-element array with units symbols for `x`, `y`, `data`
reader (function): reader function (see `pySurf.readers.instrumentReader`).
name (str): sets the name of created object.
*args, **kwargs: optional arguments for `pySurf.data2D.register_data`.
"""
# from pySurf.readers.instrumentReader import reader_dic
# pdb.set_trace()
if isinstance(data, str):
print("first argument is string, use it as filename")
file = data
data = None
# pdb.set_trace()
self.file = file # initialized to None if not provided
if file is not None:
assert data is None
# store in xrange values for x if were passed
xrange = span(x) if x is not None else None
yrange = span(y) if y is not None else None
# pdb.set_trace()
if reader is None:
reader = auto_reader(file) # returns a reader
# calling without arguments skips register, however skips also reader argumnets, temporarily arranged with pop in read_data to strip all arguments for
data, x, y = read_data(file, reader, *args, **kwargs)
# register data and pass the rest to reader
# pdb.set_trace()
if np.size(x) == data.shape[1]:
self.x = x
elif np.size(x) == 2:
# y and yrange are identical
print("WARNING: 2 element array provided for X, uses as range.")
x = np.linspace(*xrange, data.shape[1])
elif xrange is not None:
print(
"wrong number of elements for x (must be 2 or xsize_data [%i]), it is instead %i"
% (np.size(data)[1], np.size(x))
)
raise ValueError
if np.size(y) == data.shape[0]:
self.y = y
elif np.size(y) == 2:
# y and yrange are identical
print("WARNING: 2 element array provided for Y, uses as range.")
x = np.linspace(*yrange, data.shape[0])
elif yrange is not None:
print(
"wrong number of elements for y (must be 2 or ysize_data [%i]), it is instead %i"
% (np.size(data)[0], np.size(y))
)
raise ValueError
# set self.header to file header if implemented in reader, otherwise set to empty string""
try:
# kwargs['header']=True
# self.header=reader(file,header=True,*args,**kwargs)
self.header = reader(file, header=True, *args, **kwargs)
except TypeError: # unexpected keyword if header is not implemented
self.header = ""
# raise
else:
if data is not None:
if len(data.shape) != 2:
# pdb.set_trace()
print(
"WARNING: data are not bidimensional, results can be unpredictable!"
)
if x is None:
x = np.arange(data.shape[1])
if y is None:
y = np.arange(data.shape[0])
# if data is not None:
# se read_data calls register, this
data, x, y = register_data(data, x, y, *args, **kwargs)
# goes indented.
self.data, self.x, self.y = data, x, y
self.units = units
if name is not None:
self.name = name
elif file is not None:
self.name = os.path.basename(file)
else:
self.name = ""
}
],
[
csvZygo_reader,
os.path.join(pwd, testfolder,
r'input_data\zygo_data\171212_PCO2_Zygo_data.asc'), {
'strip': True,
'center': (10, 15),
'intensity': True
}
]
]
plt.ion()
#plt.close('all')
for r, f, o in tests: #reader,file,options
print('reading data %s' % os.path.basename(f))
plt.figure()
plt.subplot(121)
plot_data(*r(f))
plt.title('raw data')
plt.subplot(122)
data, x, y = read_data(f, r, **o)
plot_data(data, x, y)
plt.title('registered')
plt.suptitle(
os.path.basename(f) + ' ' +
' '.join(["%s=%s" % (k, v) for k, v in o.items()]))
plt.tight_layout()
plt.show()