def chooseStack_slot(self, fnameToChoose=False):
"""
Choose the stack to transform
can optionally load a specific file name (used for de-bugging)
"""
if fnameToChoose==False:
fileFilter="Images (*.mhd *.mha)"
fnameToChoose = QtGui.QFileDialog.getOpenFileName(self, 'Choose stack', lasHelp.readPreference('lastLoadDir'), fileFilter)
fnameToChoose = str(fnameToChoose)
if os.path.exists(fnameToChoose):
self.inputImagePath = fnameToChoose
else:
self.inputImagePath = ''
#TODO: make an alert box for this case
print "that file does not exits"
self.checkIfReadyToRun()
lasHelp.preferenceWriter('lastLoadDir', lasHelp.stripTrailingFileFromPath(fnameToChoose))
self.stackName_label.setText(fnameToChoose.split(os.path.sep)[-1])
def chooseTransform_slot(self, fnameToChoose=False):
"""
Choose the transform file to use
can optionally load a specific file name (used for de-bugging)
"""
if fnameToChoose == False:
fileFilter = "Images (*.txt)"
fnameToChoose = QtGui.QFileDialog.getOpenFileName(
self, 'Choose transform',
lasHelp.readPreference('lastLoadDir'), fileFilter)
fnameToChoose = str(fnameToChoose)
if os.path.exists(fnameToChoose):
self.transformPath = fnameToChoose
else:
self.transformPath = ''
#TODO: make an alert box for this case
print("that file does not exits")
self.checkIfReadyToRun()
lasHelp.preferenceWriter(
'lastLoadDir', lasHelp.stripTrailingFileFromPath(fnameToChoose))
self.transformName_label.setText(fnameToChoose.split(os.path.sep)[-1])
def mhd_read_raw_file(fname,header):
"""
Raw .raw file associated with the MHD header file
CAUTION: this may not adhere to MHD specs! Report bugs to author.
"""
if header.has_key('headersize'):
if header['headersize']>0:
print "\n\n **MHD reader can not currently cope with header information in .raw file. Contact the author** \n\n"
return False
#Set the endian type correctly
if header.has_key('byteorder'):
if header['byteorder'].lower == 'true' :
endian = '>' #big endian
else:
endian = '<' #little endian
else:
endian = '<' #little endian
#Set the data type correctly
if header.has_key('datatype'):
datatype = header['datatype'].lower()
if datatype == 'float':
formatType = 'f'
elif datatype == 'double':
formatType = 'd'
elif datatype == 'long':
formatType = 'l'
elif datatype == 'ulong':
formatType = 'L'
elif datatype == 'char':
formatType = 'c'
elif datatype == 'uchar':
formatType = 'B'
elif datatype == 'short':
formatType = 'h'
elif datatype == 'ushort':
formatType = 'H'
elif datatype == 'int':
formatType = 'i'
elif datatype == 'uint':
formatType = 'I'
else:
formatType = False
else:
formatType = False
if formatType == False:
print "\nCan not find data format type in MHD file. **CONTACT AUTHOR**\n"
return False
pathToFile = lasHelp.stripTrailingFileFromPath(fname)
rawFname = os.path.join(pathToFile,header['elementdatafile'])
with open(rawFname,'rb') as fid:
data = fid.read()
dimSize = header['dimsize']
#from: http://stackoverflow.com/questions/26542345/reading-data-from-a-16-bit-unsigned-big-endian-raw-image-file-in-python
fmt = endian + str(int(np.prod(dimSize))) + formatType
pix = np.asarray(struct.unpack(fmt, data))
return pix.reshape((dimSize[2],dimSize[1],dimSize[0])).swapaxes(1,2)