def _read_ydata(self, f, data, column_headers):
"""Read the y data and column headers from spc file."""
n = self._header["fnsub"]
subhdr_keys = (
"subflgs",
"subexp",
"subindx",
"subtime",
"subnext",
"subnois",
"subnpts",
"subscan",
"subwlevel",
"subresv",
)
if self._header["ftflgs"] & 1:
y_width = 2
y_fmt = "h"
divisor = 2**16
else:
y_width = 4
y_fmt = "i"
divisor = 2**32
if n * (y_width * self._pts + 32) > self._filesize - f.tell():
raise Core.StonerLoadError("No good, going to read too much data!")
for j in range(n): # We have n sub-scans
# Read the subheader and import into the main metadata dictionary as scan#:<subheader item>
subhdr = struct.unpack(b"BBHfffIIf4s", f.read(32))
subheader = dict(
zip(["scan" + str(j) + ":" + x for x in subhdr_keys], subhdr))
# Now read the y-data
exponent = subheader["scan" + str(j) + ":subexp"]
if int(exponent) & -128: # Data is unscaled direct floats
ydata = np.array(
struct.unpack(str2bytes(str(self._pts) + "f"),
f.read(self._pts * y_width)))
else: # Data is scaled by exponent
yvals = struct.unpack(str2bytes(str(self._pts) + y_fmt),
f.read(self._pts * y_width))
ydata = np.array(yvals, dtype="float64") * (2**
exponent) / divisor
data[:, j + 1] = ydata
self._header = dict(self._header, **subheader)
column_headers.append("Scan" + str(j) + ":" +
self._yvars[self._header["fytype"]])
return data
def save(self, filename=None, **kargs):
"""Overrides the save method to allow KermitPNGFiles to be written out to disc
Args:
filename (string): Filename to save as (using the same rules as for the load routines)
Keyword Arguments:
deliminator (string): Record deliniminator (defaults to a comma)
Returns:
A copy of itself.
"""
if filename is None:
filename = self.filename
if filename is None or (isinstance(filename, bool)
and not filename): # now go and ask for one
filename = self.__file_dialog("w")
metadata = PIL.PngImagePlugin.PngInfo()
for k in self.metadata:
parts = self.metadata.export(k).split("=")
key = parts[0]
val = str2bytes("=".join(parts[1:]))
metadata.add_text(key, val)
img = PIL.Image.fromarray(self.data)
img.save(filename, "png", pnginfo=metadata)
self.filename = filename
return self
def _load(self, filename=None, *args, **kargs):
"""Load an OpenGDA file.
Args:
filename (string or bool): File to load. If None then the existing filename is used,
if False, then a file dialog will be used.
Returns:
A copy of the itself after loading the data.
"""
if filename is None or not filename:
self.get_filename("r")
else:
self.filename = filename
i = 0
with io.open(self.filename, "r", errors="ignore", encoding="utf-8") as f:
for i, line in enumerate(f):
line = line.strip()
if i == 0 and line != "&SRS":
raise Core.StonerLoadError("Not a GDA File from Rasor ?" + str(line))
if "&END" in line:
break
parts = line.split("=")
if len(parts) != 2:
continue
key = parts[0]
value = parts[1].strip()
self.metadata[key] = string_to_type(value)
column_headers = f.readline().strip().split("\t")
self.data = np.genfromtxt([str2bytes(l) for l in f], dtype="float", invalid_raise=False)
self.column_headers = column_headers
return self
def save(self, filename, **kargs):
"""Overrides the save method to allow KermitPNGFiles to be written out to disc
Args:
filename (string): Filename to save as (using the same rules as for the load routines)
Keyword Arguments:
deliminator (string): Record deliniminator (defaults to a comma)
Returns:
A copy of itself.
"""
if filename is None:
filename = self.filename
if filename is None or (isinstance(filename, bool) and not filename): # now go and ask for one
filename = self.__file_dialog("w")
metadata = PIL.PngImagePlugin.PngInfo()
for k in self.metadata:
parts = self.metadata.export(k).split("=")
key = parts[0]
val = str2bytes("=".join(parts[1:]))
metadata.add_text(key, val)
img = PIL.Image.fromarray(self.data)
img.save(filename, "png", pnginfo=metadata)
self.filename = filename
return self
def _load(self, filename=None, *args, **kargs):
"""Load an OpenGDA file.
Args:
filename (string or bool): File to load. If None then the existing filename is used,
if False, then a file dialog will be used.
Returns:
A copy of the itself after loading the data.
"""
if filename is None or not filename:
self.get_filename("r")
else:
self.filename = filename
i = 0
with io.open(self.filename, "r", errors="ignore", encoding="utf-8") as f:
for i, line in enumerate(f):
line = line.strip()
if i == 0 and line != "&SRS":
raise Core.StonerLoadError("Not a GDA File from Rasor ?" + str(line))
if "&END" in line:
break
parts = line.split("=")
if len(parts) != 2:
continue
key = parts[0]
value = parts[1].strip()
self.metadata[key] = self.metadata.string_to_type(value)
if python_v3:
column_headers = f.readline().strip().split("\t")
else:
column_headers = f.next().strip().split("\t")
self.data = np.genfromtxt([str2bytes(l) for l in f], dtype="float", invalid_raise=False)
self.column_headers = column_headers
return self
def _read_ydata(self, f, data, column_headers):
"""Read the y data and column headers from spc file."""
n = self._header["fnsub"]
subhdr_keys = (
"subflgs",
"subexp",
"subindx",
"subtime",
"subnext",
"subnois",
"subnpts",
"subscan",
"subwlevel",
"subresv",
)
if self._header["ftflgs"] & 1:
y_width = 2
y_fmt = "h"
divisor = 2 ** 16
else:
y_width = 4
y_fmt = "i"
divisor = 2 ** 32
if n * (y_width * self._pts + 32) > self._filesize - f.tell():
raise Core.StonerLoadError("No good, going to read too much data!")
for j in range(n): # We have n sub-scans
# Read the subheader and import into the main metadata dictionary as scan#:<subheader item>
subhdr = struct.unpack(b"BBHfffIIf4s", f.read(32))
subheader = dict(zip(["scan" + str(j) + ":" + x for x in subhdr_keys], subhdr))
# Now read the y-data
exponent = subheader["scan" + str(j) + ":subexp"]
if int(exponent) & -128: # Data is unscaled direct floats
ydata = np.array(struct.unpack(str2bytes(str(self._pts) + "f"), f.read(self._pts * y_width)))
else: # Data is scaled by exponent
yvals = struct.unpack(str2bytes(str(self._pts) + y_fmt), f.read(self._pts * y_width))
ydata = np.array(yvals, dtype="float64") * (2 ** exponent) / divisor
data[:, j + 1] = ydata
self._header = dict(self._header, **subheader)
column_headers.append("Scan" + str(j) + ":" + self._yvars[self._header["fytype"]])
return data
def _read_xdata(self, f):
"""Read the xdata from the spc file."""
self._pts = self._header["fnpts"]
if self._header["ftflgs"] & 128: # We need to read some X Data
if 4 * self._pts > self._filesize - f.tell():
raise Core.StonerLoadError("Trying to read too much data!")
xvals = f.read(4 * self._pts) # I think storing X vals directly implies that each one is 4 bytes....
xdata = np.array(struct.unpack(str2bytes(str(self._pts) + "f"), xvals))
else: # Generate the X Data ourselves
first = self._header["ffirst"]
last = self._header["flast"]
if self._pts > 1e6: # Something not right here !
raise Core.StonerLoadError("More than 1 million points requested. Bugging out now!")
xdata = np.linspace(first, last, self._pts)
return xdata
def _read_xdata(self, f):
"""Read the xdata from the spc file."""
self._pts = self._header["fnpts"]
if self._header["ftflgs"] & 128: # We need to read some X Data
if 4 * self._pts > self._filesize - f.tell():
raise Core.StonerLoadError("Trying to read too much data!")
xvals = f.read(4 * self._pts) # I think storing X vals directly implies that each one is 4 bytes....
xdata = np.array(struct.unpack(str2bytes(str(self._pts) + "f"), xvals))
else: # Generate the X Data ourselves
first = self._header["ffirst"]
last = self._header["flast"]
if self._pts > 1e6: # Something not right here !
raise Core.StonerLoadError("More than 1 million points requested. Bugging out now!")
xdata = np.linspace(first, last, self._pts)
return xdata
def _load(self, filename=None, *args, **kargs):
"""QD system file loader routine.
Args:
filename (string or bool): File to load. If None then the existing filename is used,
if False, then a file dialog will be used.
Returns:
A copy of the itself after loading the data.
"""
if filename is None or not filename:
self.get_filename("r")
else:
self.filename = filename
setas = {}
i = 0
with io.open(self.filename, "r", encoding="utf-8", errors="ignore") as f: # Read filename linewise
for i, line in enumerate(f):
line = line.strip()
if i == 0 and line != "[Header]":
raise Core.StonerLoadError("Not a Quantum Design File !")
elif line == "[Header]" or line.startswith(";") or line == "":
continue
elif "[Data]" in line:
break
elif "," not in line:
raise Core.StonerLoadError("No data in file!")
parts = [x.strip() for x in line.split(",")]
if parts[1].split(":")[0] == "SEQUENCE FILE":
key = parts[1].split(":")[0].title()
value = parts[1].split(":")[1]
elif parts[0] == "INFO":
if parts[1] == "APPNAME":
parts[1], parts[2] = parts[2], parts[1]
if len(parts) > 2:
key = "{}.{}".format(parts[0], parts[2])
else:
raise Core.StonerLoadError("No data in file!")
key = key.title()
value = parts[1]
elif parts[0] in ["BYAPP", "FILEOPENTIME"]:
key = parts[0].title()
value = " ".join(parts[1:])
elif parts[0] == "FIELDGROUP":
key = "{}.{}".format(parts[0], parts[1]).title()
value = "[{}]".format(",".join(parts[2:]))
elif parts[0] == "STARTUPAXIS":
axis = parts[1][0].lower()
setas[axis] = setas.get(axis, []) + [int(parts[2])]
key = "Startupaxis-{}".format(parts[1].strip())
value = parts[2].strip()
else:
key = parts[0] + "," + parts[1]
key = key.title()
value = " ".join(parts[2:])
self.metadata[key] = self.metadata.string_to_type(value)
else:
raise Core.StonerLoadError("No data in file!")
if "Byapp" not in self:
raise Core.StonerLoadError("Not a Quantum Design File !")
if python_v3:
column_headers = f.readline().strip().split(",")
if "," not in f.readline():
assert False
raise Core.StonerLoadError("No data in file!")
else:
column_headers = f.next().strip().split(",")
if "," not in f.next():
raise Core.StonerLoadError("No data in file!")
data = np.genfromtxt([str2bytes(l) for l in f], dtype="float", delimiter=",", invalid_raise=False)
if data.shape[1] != len(column_headers): # Trap for buggy QD software not giving ewnough columns of data
data = np.append(data, np.ones((data.shape[0], len(column_headers) - data.shape[1])) * np.NaN, axis=1)
self.data = data
self.column_headers = column_headers
s = self.setas
for k in setas:
for ix in setas[k]:
s[ix - 1] = k
self.setas = s
return self
def _load(self, filename=None, *args, **kargs):
"""QD system file loader routine.
Args:
filename (string or bool): File to load. If None then the existing filename is used,
if False, then a file dialog will be used.
Returns:
A copy of the itself after loading the data.
"""
if filename is None or not filename:
self.get_filename("r")
else:
self.filename = filename
setas = {}
i = 0
with io.open(self.filename, "r", encoding="utf-8",
errors="ignore") as f: # Read filename linewise
for i, line in enumerate(f):
line = line.strip()
if i == 0 and line != "[Header]":
raise Core.StonerLoadError("Not a Quantum Design File !")
elif line == "[Header]" or line.startswith(";") or line == "":
continue
elif "[Data]" in line:
break
elif "," not in line:
raise Core.StonerLoadError("No data in file!")
parts = [x.strip() for x in line.split(",")]
if parts[1].split(":")[0] == "SEQUENCE FILE":
key = parts[1].split(":")[0].title()
value = parts[1].split(":")[1]
elif parts[0] == "INFO":
if parts[1] == "APPNAME":
parts[1], parts[2] = parts[2], parts[1]
if len(parts) > 2:
key = "{}.{}".format(parts[0], parts[2])
else:
raise Core.StonerLoadError("No data in file!")
key = key.title()
value = parts[1]
elif parts[0] in ["BYAPP", "FILEOPENTIME"]:
key = parts[0].title()
value = " ".join(parts[1:])
elif parts[0] == "FIELDGROUP":
key = "{}.{}".format(parts[0], parts[1]).title()
value = "[{}]".format(",".join(parts[2:]))
elif parts[0] == "STARTUPAXIS":
axis = parts[1][0].lower()
setas[axis] = setas.get(axis, []) + [int(parts[2])]
key = "Startupaxis-{}".format(parts[1].strip())
value = parts[2].strip()
else:
key = parts[0] + "," + parts[1]
key = key.title()
value = " ".join(parts[2:])
self.metadata[key] = string_to_type(value)
else:
raise Core.StonerLoadError("No data in file!")
if "Byapp" not in self:
raise Core.StonerLoadError("Not a Quantum Design File !")
column_headers = f.readline().strip().split(",")
data = np.genfromtxt([str2bytes(l) for l in f],
dtype="float",
delimiter=",",
invalid_raise=False)
if data.shape[0] == 0:
raise Core.StonerLoadError("No data in file!")
if data.shape[1] < len(
column_headers
): # Trap for buggy QD software not giving ewnough columns of data
data = np.append(
data,
np.ones(
(data.shape[0], len(column_headers) - data.shape[1])) *
np.NaN,
axis=1)
elif data.shape[1] > len(column_headers): # too much data
data = data[:, :len(column_headers) - data.shape[1]]
self.data = data
self.column_headers = column_headers
s = self.setas
for k in setas:
for ix in setas[k]:
s[ix - 1] = k
self.setas = s
return self
def save(self, filename=None, compression=zf.ZIP_DEFLATED):
"""Overrides the save method to allow ZippedFile to be written out to disc (as a mininmalist output)
Args:
filename (string or zipfile.ZipFile instance): Filename to save as (using the same rules as for the load routines)
Returns:
A copy of itself.
"""
if filename is None:
filename = self.filename
if filename is None or (isinstance(filename, bool)
and not filename): # now go and ask for one
filename = self.__file_dialog('w')
try:
if isinstance(filename,
string_types): #We;ve got a string filename
if test_is_zip(
filename
): # We can find an existing zip file somewhere in the filename
zipfile, member = test_is_zip(filename)
zipfile = zf.ZipFile(zipfile, "a")
close_me = True
elif path.exists(
filename): # The fiule exists but isn't a zip file
raise IOError(
"{} Should either be a zip file or a new zip file".
format(filename))
else: # Path doesn't exist, use extension of file part to find where the zip file should be
parts = path.split(filename)
for i, part in enumerate(parts):
if path.splitext(part)[1].lower() == ".zip":
break
else:
raise IOError(
"Can't figure out where the zip file is in {}".
format(filename))
zipfile = zf.ZipFile(path.join(*parts[:i + 1]), "w",
compression, True)
close_me = True
member = path.join("/", *parts[i + 1:])
elif isinstance(filename, zf.ZipFile
): #Handle\ zipfile instance, opening if necessary
if not filename.fp:
filename = zf.ZipFile(filename.filename, 'a')
close_me = True
else:
close_me = False
zipfile = filename
member = ""
if member == "" or member == "/": # Is our file object a bare zip file - if so create a default member name
if len(zipfile.namelist()) > 0:
member = zipfile.namelist()[-1]
self.filename = path.join(filename, member)
else:
member = "DataFile.txt"
self.filename = filename
zipfile.writestr(member, str2bytes(str(self)))
if close_me:
zipfile.close()
except Exception:
error = format_exc()
try:
zipfile.close()
except Exception:
pass
raise IOError("Error saving zipfile\n{}".format(error))
return self
