def do_plothkl(self, argument):
"""plots a section of meerkat"""
"""Has some hard coded undistortion functions in it."""
out.warn("Only poor error checking implemented!")
out.warn("Only suitable for trigonal and hexagonal crystals!")
errorcode, arguments = self.getArg(argument)
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
index = 0 # default value
if "-s" in arguments:
section = arguments[arguments.index("-s") + 1]
if "-i" in arguments:
index = arguments[arguments.index("-i") + 1]
if self.meta.format == mt.MeerkatMetaData.dtype_NORMAL:
trans = ad.Transformations(self.dataset, section)
self.currentData, x = ad.crossection_data(self.dataset, float(index), trans)
else:
slicer = mt.get_slicing_indices(section, int(index), self.meta.shape)
# be careful: the slicing in i,:,: does a weird x-y swap
self.currentData = (self.dataset['data'][slicer[0]:slicer[1],slicer[2]:slicer[3],slicer[4]:slicer[5]]).squeeze()
self.currentData = np.tile(self.currentData, (1,1))
# the following block is the hard coded undistortion of my trigonal crystals
if section == "hkx":
self.currentData = ad.hextransform(self.currentData)
elif section == "xkl" or section == "hxl":
# counteracting the weird slicing
a = math.radians(90)
T = np.array([[math.cos(a), math.sin(a)],[-math.sin(a), math.cos(a)]])
self.currentData = ad.imtransform_centered(self.currentData, T)
self.replot()
elif errorcode == ERROR_NO_ARGUMENTS:
out.error("No arguments supplied!")
def do_openFile(self, argument):
"""Opens a given file."""
errorcode, arguments = self.getArg(argument)
filename = "reconstruction.h5" # a default filename is assumed
filealias = "default" # a default name is assumed
if errorcode != ERROR_ODD_ARGUMENTS:
if "-n" in arguments:
filename = arguments[arguments.index("-n") + 1]
else:
out.warn("No file name is given! Trying default name \"" + filename + "\".")
if "-a" in arguments:
filealias = arguments[arguments.index("-a") + 1]
if os.path.isfile(filename):
#TODO:requires replacement with arkadiy's routine
file = h5py.File(filename, 'r')
out.okay("File successfully opened as " + filealias + "!")
self.activeDset = filealias
pyplot.close("all") # to prevent display issues
if filealias in self.dsetName:
self.dset[self.dsetName.index(filealias)] = file
else:
self.dset.append(file)
self.dsetName.append(filealias)
self.meta = mt.MeerkatMetaData(self.dataset)
out.warn("Active data set is now " + filealias)
else:
out.error("File \"" + filename + "\" does not exist!")
def do_info(self, argument):
"""Prints the meta data."""
if self.meta != None:
errorcode, arguments = self.getArg(argument)
if errorcode != self.CODE_ODD_ARGUMENTS:
options = "nafsit"
if "-p" in arguments:
options = arguments[arguments.index("-p") + 1]
if "n" in options:
print("Active file name: %s" %
os.path.split(self.dataset.filename)[1])
if "a" in options:
print("Active file alias: %s" % self.activeDset)
if "f" in options: print("File format: %s" % self.meta.format)
if "s" in options:
print("Pixel dimensions: x = %s, y = %s, z = %s" %
tuple(self.meta.shape))
if self.meta.format == mt.MeerkatMetaData.dtype_NORMAL: # others do not have the fields
if "i" in options:
print("Pixel dimensions: h = %s, k = %s, l = %s" %
tuple(self.meta.hklRange))
if "t" in options:
print(
"Pixel dimensions: h/x = %s, k/y = %s, l/z = %s" %
tuple(self.meta.steps))
else:
out.error("Open a data file first!")
def help_openFile(self):
"""openFile help page entry."""
print("Opens a h5 file, either in meerkat or direct format.")
out.error("Only meerkat data format implemented at the moment!")
print("Arguments:")
print("\t-n <file name>\tspecifies the file name, if not given \"reconstruction.h5\" is assumed.")
print("\t-a <file alias>\tspecifies the alias for the data under which it can be called , if not given \"default\" is assumed.")
def do_openFile(self, argument):
"""Opens a given file."""
errorcode, arguments = self.getArg(argument)
filename = "reconstruction.h5" # a default filename is assumed
filealias = "default" # a default name is assumed
if errorcode != ERROR_ODD_ARGUMENTS:
if "-n" in arguments:
filename = arguments[arguments.index("-n") + 1]
else:
out.warn("No file name is given! Trying default name \"" +
filename + "\".")
if "-a" in arguments:
filealias = arguments[arguments.index("-a") + 1]
if os.path.isfile(filename):
#TODO:requires replacement with arkadiy's routine
file = h5py.File(filename, 'r')
out.okay("File successfully opened as " + filealias + "!")
self.activeDset = filealias
pyplot.close("all") # to prevent display issues
if filealias in self.dsetName:
self.dset[self.dsetName.index(filealias)] = file
else:
self.dset.append(file)
self.dsetName.append(filealias)
self.meta = mt.MeerkatMetaData(self.dataset)
out.warn("Active data set is now " + filealias)
else:
out.error("File \"" + filename + "\" does not exist!")
def do_saveData(self, argument):
"""Saves the last displayed image as a csv file."""
errorcode, arguments = self.getArg(argument)
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-o" in arguments:
outfile = arguments[arguments.index("-o") + 1]
data = np.asarray(self.currentData)
np.savetxt(outfile, data, delimiter=";")
out.okay("Successfully saved as " + outfile + "!")
else:
out.error("No output name given!")
def help_openFile(self):
"""openFile help page entry."""
print("Opens a h5 file, either in meerkat or direct format.")
out.error("Only meerkat data format implemented at the moment!")
print("Arguments:")
print(
"\t-n <file name>\tspecifies the file name, if not given \"reconstruction.h5\" is assumed."
)
print(
"\t-a <file alias>\tspecifies the alias for the data under which it can be called , if not given \"default\" is assumed."
)
def do_saveData(self, argument):
"""Saves the last displayed image as a csv file."""
errorcode, arguments = self.getArg(argument)
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-o" in arguments:
outfile = arguments[arguments.index("-o") + 1]
data = np.asarray(self.currentData)
np.savetxt(outfile, data, delimiter=";")
out.okay("Successfully saved as " + outfile + "!")
else:
out.error("No output name given!")
def getArg(self, line):
"""Splits the arguments and checks if the correct number of arguments are given."""
errorcode = NO_ERROR
arguments = str(line).split()
if len(arguments) == 0: #no arguments supplied
arguments = ""
errorcode = ERROR_NO_ARGUMENTS
elif len(arguments) % 2 != 0: #invalid number of arguments
arguments = ""
errorcode = ERROR_ODD_ARGUMENTS
out.error("Invalid number of arguments!")
return errorcode, arguments
def getArg(self, line):
"""Splits the arguments and checks if the correct number of arguments are given."""
errorcode = NO_ERROR
arguments = str(line).split()
if len(arguments) == 0: #no arguments supplied
arguments = ""
errorcode = ERROR_NO_ARGUMENTS
elif len(arguments) % 2 != 0: #invalid number of arguments
arguments = ""
errorcode = ERROR_ODD_ARGUMENTS
out.error("Invalid number of arguments!")
return errorcode, arguments
def do_saveImage(self, argument):
"""Saves the last displayed image as a csv file."""
errorcode, arguments = self.getArg(argument)
if self.currentImage != None:
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-o" in arguments:
outfile = arguments[arguments.index("-o") + 1]
self.currentImage.save(outfile)
out.okay("Successfully saved as " + outfile + "!")
else:
out.error("No output name given!")
else:
out.error("No image in buffer to save!")
def do_saveImage(self, argument):
"""Saves the last displayed image as a csv file."""
errorcode, arguments = self.getArg(argument)
if self.currentImage != None:
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-o" in arguments:
outfile = arguments[arguments.index("-o") + 1]
self.currentImage.save(outfile)
out.okay("Successfully saved as " + outfile + "!")
else:
out.error("No output name given!")
else:
out.error("No image in buffer to save!")
def do_layout(self, argument):
"""Changes the layout of pyplot."""
errorcode, arguments = self.getArg(argument)
if self.activeDset != None:
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-min" in arguments:
self.contrast_min = float(
arguments[arguments.index("-min") + 1])
if "-max" in arguments:
self.contrast_max = float(
arguments[arguments.index("-max") + 1])
if "-c" in arguments:
self.cmap_selection = int(arguments[arguments.index("-c") +
1])
if self.cmap_selection >= len(
self.cmaps) or self.cmap_selection < 0:
out.error("Unknown color map index.")
self.cmap_selection = 0
out.warn("Color map set to default.")
if "-scale" in arguments:
if (arguments[arguments.index("-scale") + 1]
== self.LIN_SCALE) or (
arguments[arguments.index("-scale") + 1]
== self.LOG_SCALE):
self.plotscale = arguments[arguments.index("-scale") +
1]
else:
out.error("Unknown scale!")
self.replot()
elif errorcode != ERROR_NO_ARGUMENTS:
out.error("Input required!")
else:
out.error("No data selected!")
def do_layout(self, argument):
"""Changes the layout of pyplot."""
errorcode, arguments = self.getArg(argument)
if self.activeDset != None:
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-min" in arguments:
self.contrast_min = float(arguments[arguments.index("-min") + 1])
if "-max" in arguments:
self.contrast_max = float(arguments[arguments.index("-max") + 1])
if "-c" in arguments:
self.cmap_selection = int(arguments[arguments.index("-c") + 1])
if self.cmap_selection >= len(self.cmaps) or self.cmap_selection < 0:
out.error("Unknown color map index.")
self.cmap_selection = 0
out.warn("Color map set to default.")
if "-scale" in arguments:
if (arguments[arguments.index("-scale") + 1] == self.LIN_SCALE) or (arguments[arguments.index("-scale") + 1] == self.LOG_SCALE):
self.plotscale = arguments[arguments.index("-scale") + 1]
else:
out.error("Unknown scale!")
self.replot()
elif errorcode != ERROR_NO_ARGUMENTS:
out.error("Input required!")
else:
out.error("No data selected!")
def do_info(self, argument):
"""Prints the meta data."""
if self.meta != None:
errorcode, arguments = self.getArg(argument)
if errorcode != self.CODE_ODD_ARGUMENTS:
options = "nafsit"
if "-p" in arguments:
options = arguments[arguments.index("-p") + 1]
if "n" in options: print("Active file name: %s" % os.path.split(self.dataset.filename)[1])
if "a" in options: print("Active file alias: %s" % self.activeDset)
if "f" in options: print("File format: %s" % self.meta.format)
if "s" in options: print("Pixel dimensions: x = %s, y = %s, z = %s" % tuple(self.meta.shape))
if self.meta.format == mt.MeerkatMetaData.dtype_NORMAL: # others do not have the fields
if "i" in options: print("Pixel dimensions: h = %s, k = %s, l = %s" % tuple(self.meta.hklRange))
if "t" in options: print("Pixel dimensions: h/x = %s, k/y = %s, l/z = %s" % tuple(self.meta.steps))
else:
out.error("Open a data file first!")
def do_setActive(self, argument):
"""Activates a dataset."""
errorcode, arguments = self.getArg(argument)
alias = "default" #default value
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-a" in arguments:
alias = arguments[arguments.index("-a") + 1]
else:
out.warn("No arguments supplied, trying default.")
if alias in self.dsetName:
self.activeDset = alias
self.meta = mt.MeerkatMetaData(self.dataset)
pyplot.close("all") #in order to prevent display issues
out.okay("Activated " + alias + "!")
else:
out.error(alias + " not found!")
elif errorcode == ERROR_NO_ARGUMENTS:
out.error("No arguments supplied!")
def do_setActive(self, argument):
"""Activates a dataset."""
errorcode, arguments = self.getArg(argument)
alias = "default" #default value
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
if "-a" in arguments:
alias = arguments[arguments.index("-a") + 1]
else:
out.warn("No arguments supplied, trying default.")
if alias in self.dsetName:
self.activeDset = alias
self.meta = mt.MeerkatMetaData(self.dataset)
pyplot.close("all") #in order to prevent display issues
out.okay("Activated " + alias + "!")
else:
out.error(alias + " not found!")
elif errorcode == ERROR_NO_ARGUMENTS:
out.error("No arguments supplied!")
def do_plothkl(self, argument):
"""plots a section of meerkat"""
"""Has some hard coded undistortion functions in it."""
out.warn("Only poor error checking implemented!")
out.warn("Only suitable for trigonal and hexagonal crystals!")
errorcode, arguments = self.getArg(argument)
if errorcode != ERROR_NO_ARGUMENTS and errorcode != ERROR_ODD_ARGUMENTS:
index = 0 # default value
if "-s" in arguments:
section = arguments[arguments.index("-s") + 1]
if "-i" in arguments:
index = arguments[arguments.index("-i") + 1]
if self.meta.format == mt.MeerkatMetaData.dtype_NORMAL:
trans = ad.Transformations(self.dataset, section)
self.currentData, x = ad.crossection_data(
self.dataset, float(index), trans)
else:
slicer = mt.get_slicing_indices(section, int(index),
self.meta.shape)
# be careful: the slicing in i,:,: does a weird x-y swap
self.currentData = (
self.dataset['data'][slicer[0]:slicer[1],
slicer[2]:slicer[3],
slicer[4]:slicer[5]]).squeeze()
self.currentData = np.tile(self.currentData, (1, 1))
# the following block is the hard coded undistortion of my trigonal crystals
if section == "hkx":
self.currentData = ad.hextransform(self.currentData)
elif section == "xkl" or section == "hxl":
# counteracting the weird slicing
a = math.radians(90)
T = np.array([[math.cos(a), math.sin(a)],
[-math.sin(a), math.cos(a)]])
self.currentData = ad.imtransform_centered(self.currentData, T)
self.replot()
elif errorcode == ERROR_NO_ARGUMENTS:
out.error("No arguments supplied!")
def plot2img(self, figure):
"""Converts a pyplot figure into a PIL image by the use of the buffer."""
buf = io.BytesIO()
pyplot.savefig(buf, format='png')
buf.seek(0)
return Image.open(buf)
#offblock
#end of internal functions
#offblock
if __name__ == '__main__':
"""Main loop creation, can run in terminal mode or script mode."""
if len(
sys.argv
) == 2: # in this case, it is assumed that the user provides a file with a list of commands
input = open(sys.argv[1], 'rt')
try:
# setting up silent script mode
interpreter = Burrow(stdin=input)
interpreter.use_rawinput = False # required for file input to read new lines etc correctly
interpreter.prompt = "" # silent mode
interpreter.cmdloop()
finally:
input.close()
elif len(sys.argv) == 1: # plain old commandline
interpreter = Burrow()
interpreter.cmdloop()
else:
out.error("Wrong input, <none> or <script filename> expected!")
pyplot.show()
#onblock convertion of images und plots
def plot2img(self, figure):
"""Converts a pyplot figure into a PIL image by the use of the buffer."""
buf = io.BytesIO()
pyplot.savefig(buf, format='png')
buf.seek(0)
return Image.open(buf)
#offblock
#end of internal functions
#offblock
if __name__ == '__main__':
"""Main loop creation, can run in terminal mode or script mode."""
if len(sys.argv) == 2: # in this case, it is assumed that the user provides a file with a list of commands
input = open(sys.argv[1], 'rt')
try:
# setting up silent script mode
interpreter = Burrow(stdin=input)
interpreter.use_rawinput = False # required for file input to read new lines etc correctly
interpreter.prompt = "" # silent mode
interpreter.cmdloop()
finally:
input.close()
elif len(sys.argv) == 1: # plain old commandline
interpreter = Burrow()
interpreter.cmdloop()
else:
out.error("Wrong input, <none> or <script filename> expected!")