def SaveGeometry(self, filename=None):
"""Save the geometry to a file"""
if filename is None:
self._filename = EVSFileDialog.asksaveasfilename(
message="Save Surface", filetypes=self._ft, defaultfile="surface.vtp", defaultextension="*.vtp"
)
else:
self._filename = filename
if self._filename:
try:
self._writer.SetFileName(self._filename)
except AttributeError, msg:
logging.exception("IsoSurfaceDisplay")
dlg = wx.MessageDialog(self._Dialog, str(msg), "Error", wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
self._writer.SetInputConnection(
self._app_states[self._current_image_index].GetFactory().GetInputConnection()
)
try:
with wx.BusyCursor():
event.notify(ProgressEvent("Saving surface...", 0.0))
self._writer.Write()
event.notify(ProgressEvent("Saving surface...", 1.0))
logging.info("Surface saved to '{0}'".format(self._filename))
except IOError, (errno, strerror):
logging.exception("IsoSurfaceDisplay")
dlg = wx.MessageDialog(
self._Dialog, "[Errno %d]: %s" % (errno, strerror), "Error", wx.OK | wx.ICON_ERROR
)
dlg.ShowModal()
dlg.Destroy()
def SaveData(self, e=None, filename=""):
"""Save line/histogram data to a text file"""
ft = collections.OrderedDict([])
ft["text files"] = ["*.txt"]
curr_dir = self.GetCurrentDirectory()
if filename == "":
filename = EVSFileDialog.asksaveasfilename(
message='Save Line Data', filetypes=ft, defaultdir=curr_dir, defaultextension='.txt')
if not filename:
return
self.SaveCurrentDirectory(os.path.dirname(filename))
_file = open(filename, 'wt')
# write out a header
_file.write('#\n')
_file.write('# Creation Date: %s\n' %
datetime.datetime.now().isoformat())
if self.filename:
filename = self.filename.encode(
sys.getfilesystemencoding() or 'UTF-8')
else:
filename = '(unknown)'
_file.write('# Image filename: %s\n' % filename)
_file.write('# MicroView Software Version: %s\n' % PACKAGE_VERSION)
_file.write('# MicroView Software SHA1: %s\n' % PACKAGE_SHA1)
_file.write('#\n')
n = len(self.xdata)
numC = self.ydata.shape[-1]
_format = '%f\t' + (numC - 1) * '%f\t' + '%f\n'
_file.write(self.file_label + '\n')
for xval, yval in zip(self.xdata, self.ydata):
# take care -- yval could be from a multichannel image
l = [xval]
l.extend(yval)
_file.write(_format % tuple(l))
_file.close()
def SavePointsToFile(self):
if self._Mark1IsSet == 0 or self._Mark2IsSet == 0:
return
results_logger = logging.getLogger('results')
# Get a filename to save points to
ft = collections.OrderedDict()
ft["text file"] = ["*.txt", "*.TXT"]
curr_dir = self.GetCurrentDirectory()
filename = EVSFileDialog.asksaveasfilename(
message='Save Points', filetypes=ft, defaultdir=curr_dir, defaultextension='.txt')
pt1 = self.GetFirstPoint()
pt2 = self.GetSecondPoint()
origin = self._ImageData.GetOrigin()
spacing = self._ImageData.GetSpacing()
if self._sMeasurementUnit == "mm":
pt1 = (round(pt1[0], 3), round(pt1[1], 3), round(pt1[2], 3))
pt2 = (round(pt2[0], 3), round(pt2[1], 3), round(pt2[2], 3))
str1 = "(%0.3f,%0.3f,%0.3f) (%0.3f,%0.3f,%0.3f) (mm)" % (pt1[0], pt1[1], pt1[2],
pt2[0], pt2[1], pt2[2])
else:
pt1 = (round(pt1[0], 3), round(pt1[1], 3), round(pt1[2], 3))
pt2 = (round(pt2[0], 3), round(pt2[1], 3), round(pt2[2], 3))
pt1 = ((pt1[0] - origin[0]) / spacing[0], (pt1[1] - origin[
1]) / spacing[1], (pt1[2] - origin[2]) / spacing[2])
pt2 = ((pt2[0] - origin[0]) / spacing[0], (pt2[1] - origin[
1]) / spacing[1], (pt2[2] - origin[2]) / spacing[2])
str1 = "(%0.1f,%0.1f,%0.1f) (%0.1f,%0.1f,%0.1f) (%s)" % (
pt1[0], pt1[1], pt1[2], pt2[0], pt2[1], pt2[2], "pixels")
if filename:
try:
file = open(filename, 'at')
file.write(str1)
file.write("\n")
file.close()
results_logger.info(str1)
logging.info("Saved line length to '%s'" % filename)
except:
pass
def SaveGeometry(self, filename=None):
"""Save the geometry to a file"""
if filename is None:
self._filename = EVSFileDialog.asksaveasfilename(
message='Save Surface',
filetypes=self._ft,
defaultfile='surface.vtp',
defaultextension='*.vtp')
else:
self._filename = filename
if self._filename:
try:
self._writer.SetFileName(self._filename)
except AttributeError, msg:
logging.exception("IsoSurfaceDisplay")
dlg = wx.MessageDialog(self._Dialog, str(msg), 'Error',
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
self._writer.SetInputConnection(self._app_states[
self._current_image_index].GetFactory().GetInputConnection())
try:
with wx.BusyCursor():
event.notify(ProgressEvent("Saving surface...", 0.0))
self._writer.Write()
event.notify(ProgressEvent("Saving surface...", 1.0))
logging.info("Surface saved to '{0}'".format(
self._filename))
except IOError, (errno, strerror):
logging.exception("IsoSurfaceDisplay")
dlg = wx.MessageDialog(self._Dialog,
"[Errno %d]: %s" % (errno, strerror),
'Error', wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
def SaveLineGrayScaleValues(self, fmt):
if (self._Mark1IsSet != 1) or (self._Mark2IsSet != 1):
return
x1, y1, z1 = self._Mark1.GetPosition()
x2, y2, z2 = self._Mark2.GetPosition()
# calculate the length of the line in pixels
spacing = self._ImageData.GetSpacing()
LineLength = math.sqrt(math.pow((x1 - x2) / spacing[0], 2) +
math.pow((y1 - y2) / spacing[1], 2) +
math.pow((z1 - z2) / spacing[2], 2))
line = vtk.vtkLineSource()
line.SetPoint1(x1, y1, z1)
line.SetPoint2(x2, y2, z2)
if LineLength < 100:
NumSegments = 100
else:
NumSegments = math.ceil(LineLength)
line.SetResolution(NumSegments)
line.Update()
ft = collections.OrderedDict()
ft["text file"] = ["*.txt", "*.TXT"]
curr_dir = self.GetCurrentDirectory()
filename = EVSFileDialog.asksaveasfilename(
message='Save Points', filetypes=ft, defaultdir=curr_dir, defaultextension='.txt')
if not filename:
return
curr_dir = os.path.dirname(os.path.abspath(filename))
if filename:
self.SaveCurrentDirectory(os.path.abspath(curr_dir))
if filename:
if os.path.splitext(filename)[-1].lower() != '.txt':
filename += ".txt"
_file = open(filename, 'wt')
# Write the header.
self.WriteFileHeader(_file)
origin = self._ImageData.GetOrigin()
if self._sMeasurementUnit == "mm":
# Calculate the length of the line in mm
LineLength = math.sqrt(math.pow(x1 - x2, 2) + math.pow(
y1 - y2, 2) + math.pow(z1 - z2, 2))
# Calculate point size in mm
PointSize = LineLength / float(NumSegments)
_file.write('# %s: %4.3f mm\n' % ("Line Length", LineLength))
_file.write('# %s: (%4.3f, %4.3f, %4.3f) mm\n' % ("Point 1",
x1 -
origin[0],
y1 -
origin[1],
z1 - origin[2]))
_file.write('# %s: (%4.3f, %4.3f, %4.3f) mm\n' % ("Point 2",
x2 -
origin[0],
y2 -
origin[1],
z2 - origin[2]))
_file.write('# %s: %7.6f\n#\n' % ("Point Size", PointSize))
else:
# Calculate point size in pixels
PointSize = LineLength / float(NumSegments)
s = self._ImageData.GetSpacing()
_file.write('# %s: %4.3f %s\n' % (
"Line Length", LineLength, "pixels"))
_file.write('# %s: (%2.1f, %2.1f, %2.1f) %s\n' % ("Point 1",
(x1 - origin[
0]) / (
float)(
s[0]),
(y1 - origin[
1]) / (
float)(
s[1]),
(z1 - origin[2]) / (
float)(
s[2]),
"pixels"))
_file.write('# %s: (%2.1f, %2.1f, %2.1f) %s\n' % ("Point 2",
(x2 - origin[0]) / (
float)(
s[0]),
(y2 - origin[1]) / (
float)(
s[1]),
(z2 - origin[2]) / (
float)(
s[2]),
"pixels"))
_file.write('# %s: %7.6f %s\n' % (
"Point Size", PointSize, "pixels"))
# Write the data.
numScalars = line.GetOutput().GetNumberOfPoints()
for n in range(numScalars):
point = line.GetOutput().GetPoint(n)
GrayScaleValue = self.TriLinearInterpolation(
point[0], point[1], point[2])
if fmt:
_file.write("%7.6f, %s" % (
PointSize * n, str(GrayScaleValue)))
else:
_file.write(str(GrayScaleValue))
if n != NumSegments:
if fmt:
_file.write("\n")
else:
_file.write(",")
_file.close()