def OnButtonNextTask(self, evt):
overwrite = self.check_box.IsChecked()
algorithm = 'Default'
options = {}
to_generate = True
if self.GetMaskSelected() != -1:
sl = slice_.Slice()
if sl.current_mask.was_edited:
dlgs = dlg.SurfaceDialog()
if dlgs.ShowModal() == wx.ID_OK:
algorithm = dlgs.GetAlgorithmSelected()
options = dlgs.GetOptions()
else:
to_generate = False
dlgs.Destroy()
if to_generate:
mask_index = sl.current_mask.index
method = {'algorithm': algorithm,
'options': options}
srf_options = {"index": mask_index,
"name": '',
"quality": _('Optimal *'),
"fill": False,
"keep_largest": False,
"overwrite": overwrite}
Publisher.sendMessage('Create surface from index',
{'method': method, 'options': srf_options})
Publisher.sendMessage('Fold surface task')
else:
dlg.InexistentMask()
def OnClutChange(self, evt):
Publisher.sendMessage(
'Change colour table from background image from widget',
evt.GetNodes())
slc = sl.Slice()
Publisher.sendMessage('Update window level value',
(slc.window_width, slc.window_level))
def OnButtonInfo(self, evt):
sl = slice_.Slice()
overlay_data = sl.overlay
if overlay_data is not None:
ovdlg = dlg.OverlayDialog(overlay_data)
ovdlg.Show()
def OnOpenOverlay(self, pubsub_evt):
dirpath = dialog.ShowOpenNiftiDialog()
nifti_image = nifti.ReadNifti(dirpath)
if nifti_image:
# Rearranges the axes of the image to be closest to RAS+ orientation,
# so the slices of the image (axial, coronal, sagittal) are shown correctly.
# See http://nipy.org/nibabel/image_orientation.html
nifti_image = as_closest_canonical(nifti_image)
imagedata = nifti_image.get_data()
# Conversion of type of numpy array (to unsigned char)
imagedata = imagedata.astype('f')
slc = sl.Slice()
y, x = slc.buffer_slices["AXIAL"].image.shape
z = slc.buffer_slices["SAGITAL"].image.shape[0]
# Add borders (with zero values) to overlay array to fit the dimensions of the 3D image
pad_x = numpy.abs((x / 2.0) - (imagedata.shape[0] / 2.0))
pad_y = numpy.abs((y / 2.0) - (imagedata.shape[1] / 2.0))
pad_z = numpy.abs((z / 2.0) - (imagedata.shape[2] / 2.0))
final_overlay = numpy.pad(imagedata,
((pad_x, pad_x), (pad_y, pad_y),
(pad_z, pad_z)),
mode='constant',
constant_values=0)
# Modifications to work with Invesalius (Z,Y,X)
final_overlay = numpy.swapaxes(final_overlay, 0, 2)
final_overlay = numpy.fliplr(final_overlay)
Publisher.sendMessage('Set slice overlay', final_overlay)
def LoadProject(self):
proj = prj.Project()
const.THRESHOLD_OUTVALUE = proj.threshold_range[0]
const.THRESHOLD_INVALUE = proj.threshold_range[1]
const.WINDOW_LEVEL[_('Default')] = (proj.window, proj.level)
const.WINDOW_LEVEL[_('Manual')] = (proj.window, proj.level)
self.Slice = sl.Slice()
self.Slice.spacing = proj.spacing
Publisher.sendMessage('Load slice to viewer',
(proj.mask_dict))
Publisher.sendMessage('Load slice plane')
Publisher.sendMessage('Bright and contrast adjustment image',\
(proj.window, proj.level))
Publisher.sendMessage('Update window level value',\
(proj.window, proj.level))
Publisher.sendMessage('Set project name', proj.name)
Publisher.sendMessage('Load surface dict',
proj.surface_dict)
Publisher.sendMessage('Hide surface items',
proj.surface_dict)
self.LoadImagedataInfo() # TODO: where do we insert this <<<?
Publisher.sendMessage('Show content panel')
Publisher.sendMessage('Update AUI')
if len(proj.mask_dict):
mask_index = len(proj.mask_dict) -1
for m in proj.mask_dict.values():
Publisher.sendMessage('Add mask',
(m.index, m.name,
m.threshold_range, m.colour))
self.Slice.current_mask = proj.mask_dict[mask_index]
Publisher.sendMessage('Show mask', (mask_index, True))
else:
mask_name = const.MASK_NAME_PATTERN % (1,)
thresh = const.THRESHOLD_RANGE
colour = const.MASK_COLOUR[0]
Publisher.sendMessage('Create new mask',
(mask_name, thresh, colour))
Publisher.sendMessage('Load measurement dict',
(proj.measurement_dict, self.Slice.spacing))
Publisher.sendMessage(('Set scroll position', 'AXIAL'),proj.matrix_shape[0]/2)
Publisher.sendMessage(('Set scroll position', 'SAGITAL'),proj.matrix_shape[1]/2)
Publisher.sendMessage(('Set scroll position', 'CORONAL'),proj.matrix_shape[2]/2)
Publisher.sendMessage('End busy cursor')
def UpdateWindowLevelValue(self, pubsub_evt):
window, level = pubsub_evt.data
self.acum_achange_window, self.acum_achange_level = (window, level)
self.SetWLText(window, level)
slc = sl.Slice()
slc._update_wwwl_widget_nodes(window, level)
Publisher.sendMessage('Update all slice')
Publisher.sendMessage('Update clut imagedata widget')
def SetLayout(self, layout):
self.layout = layout
if (layout == (1, 1)) and self.on_text:
self.ShowTextActors()
else:
self.HideTextActors(change_status=False)
slice_ = sl.Slice()
self.LoadRenderers(slice_.GetOutput())
self.__configure_renderers()
self.__configure_scroll()
def SetInput(self, mask_dict):
self.slice_ = sl.Slice()
max_slice_number = sl.Slice().GetNumberOfSlices(self.orientation)
self.scroll.SetScrollbar(wx.SB_VERTICAL, 1, max_slice_number,
max_slice_number)
self.slice_data = self.create_slice_window()
self.slice_data.SetCursor(self.__create_cursor())
self.cam = self.slice_data.renderer.GetActiveCamera()
self.__build_cross_lines()
# Set the slice number to the last slice to ensure the camera is far
# enough to show all slices.
self.set_slice_number(max_slice_number - 1)
self.__update_camera()
self.slice_data.renderer.ResetCamera()
self.interactor.GetRenderWindow().AddRenderer(self.slice_data.renderer)
self.interactor.Render()
self.EnableText()
self.wl_text.Hide()
## Insert cursor
self.SetInteractorStyle(const.STATE_DEFAULT)
def OnNew(self):
sl = slice_.Slice()
dialog = dlg.SurfaceCreationDialog(
None, -1, _('New surface'), mask_edited=sl.current_mask.was_edited)
try:
if dialog.ShowModal() == wx.ID_OK:
ok = 1
else:
ok = 0
except (wx._core.PyAssertionError): #TODO FIX: win64
ok = 1
if ok:
surface_options = dialog.GetValue()
Publisher.sendMessage('Create surface from index', surface_options)
dialog.Destroy()
def OnLinkNewSurface(self, evt=None):
#import gui.dialogs as dlg
sl = slice_.Slice()
dialog = dlg.SurfaceCreationDialog(None, -1,
_('New surface'),
mask_edited=sl.current_mask.was_edited)
try:
if dialog.ShowModal() == wx.ID_OK:
ok = 1
else:
ok = 0
except(wx._core.PyAssertionError): #TODO FIX: win64
ok = 1
if (ok):
## Retrieve information from dialog
#(mask_index, surface_name, surface_quality, fill_holes,\
#keep_largest) = dialog.GetValue()
## Retrieve information from mask
#proj = prj.Project()
#mask = proj.mask_dict[mask_index]
## Send all information so surface can be created
#surface_data = [proj.imagedata,
#mask.colour,
#mask.threshold_range,
#mask.edited_points,
#False, # overwrite
#surface_name,
#surface_quality,
#fill_holes,
#keep_largest]
surface_options = dialog.GetValue()
Publisher.sendMessage('Create surface from index', surface_options)
dialog.Destroy()
if evt:
evt.Skip()
def CreateNiftiProject(self, imagedata):
header = imagedata.get_header()
proj = prj.Project()
proj.imagedata = None
proj.name = _("Untitled")
proj.SetAcquisitionModality("MRI")
#TODO: Verify if all Nifti are in AXIAL orientation
# To get Z, X, Y (used by InVesalius), not X, Y, Z
matrix, matrix_filename = image_utils.nifti2mmap(imagedata)
# if header['orient'] == 0:
# proj.original_orientation = const.AXIAL
# elif header['orient'] == 1:
# proj.original_orientation = const.CORONAL
# elif header['orient'] == 2:
# proj.original_orientation = const.SAGITAL
# else:
# proj.original_orientation = const.SAGITAL
# Project orientation set CORONAL as default
proj.original_orientation = const.CORONAL
proj.threshold_range = (numpy.amin(matrix), numpy.amax(matrix))
proj.window = proj.threshold_range[1] - proj.threshold_range[0]
proj.level = (0.5 *
(proj.threshold_range[1] + proj.threshold_range[0]))
proj.spacing = header['pixdim'][1:4]
proj.matrix_shape = matrix.shape
self.Slice = sl.Slice()
self.Slice.matrix = matrix
self.Slice.matrix_filename = matrix_filename
self.Slice.window_level = proj.level
self.Slice.window_width = proj.window
self.Slice.spacing = header.get_zooms()[:3]
Publisher.sendMessage('Update threshold limits list',
proj.threshold_range)
def OpenProject(self, filepath):
Publisher.sendMessage('Begin busy cursor')
path = os.path.abspath(filepath)
proj = prj.Project()
proj.OpenPlistProject(path)
proj.SetAcquisitionModality(proj.modality)
self.Slice = sl.Slice()
self.Slice._open_image_matrix(proj.matrix_filename,
tuple(proj.matrix_shape),
proj.matrix_dtype)
self.Slice.window_level = proj.level
self.Slice.window_width = proj.window
Publisher.sendMessage('Update threshold limits list',
proj.threshold_range)
self.LoadProject()
session = ses.Session()
session.OpenProject(filepath)
Publisher.sendMessage("Enable state project", True)
def CreateAnalyzeProject(self, imagedata):
header = imagedata.get_header()
proj = prj.Project()
proj.imagedata = None
proj.name = _("Untitled")
proj.SetAcquisitionModality("MRI")
#TODO: Verify if all Analyze are in AXIAL orientation
# To get Z, X, Y (used by InVesalius), not X, Y, Z
matrix, matrix_filename = image_utils.analyze2mmap(imagedata)
if header['orient'] == 0:
proj.original_orientation = const.AXIAL
elif header['orient'] == 1:
proj.original_orientation = const.CORONAL
elif header['orient'] == 2:
proj.original_orientation = const.SAGITAL
else:
proj.original_orientation = const.SAGITAL
proj.threshold_range = (header['glmin'], header['glmax'])
# Window level and wide are normalized to best visualization experience in NIFTI
proj.window = proj.threshold_range[1] - proj.threshold_range[0]
proj.level = (0.5 *
(proj.threshold_range[1] + proj.threshold_range[0]))
proj.spacing = header['pixdim'][1:4]
proj.matrix_shape = matrix.shape
self.Slice = sl.Slice()
self.Slice.matrix = matrix
self.Slice.matrix_filename = matrix_filename
self.Slice.window_level = proj.level
self.Slice.window_width = proj.window
self.Slice.spacing = header.get_zooms()[:3]
Publisher.sendMessage('Update threshold limits list',
proj.threshold_range)
def OnUpdateScroll(self, pubsub_evt):
max_slice_number = sl.Slice().GetNumberOfSlices(self.orientation)
self.scroll.SetScrollbar(wx.SB_VERTICAL, 1, max_slice_number,
max_slice_number)
def OpenDicomGroup(self, dicom_group, interval, file_range, gui=True):
# Retrieve general DICOM headers
dicom = dicom_group.GetDicomSample()
# Create imagedata
interval += 1
filelist = dicom_group.GetFilenameList()[::interval]
if not filelist:
utils.debug("Not used the IPPSorter")
filelist = [i.image.file for i in dicom_group.GetHandSortedList()[::interval]]
if file_range != None and file_range[1] > file_range[0]:
filelist = filelist[file_range[0]:file_range[1] + 1]
zspacing = dicom_group.zspacing * interval
size = dicom.image.size
bits = dicom.image.bits_allocad
sop_class_uid = dicom.acquisition.sop_class_uid
xyspacing = dicom.image.spacing
orientation = dicom.image.orientation_label
if sop_class_uid == '1.2.840.10008.5.1.4.1.1.7': #Secondary Capture Image Storage
use_dcmspacing = 1
else:
use_dcmspacing = 0
imagedata = None
sx, sy = size
n_slices = len(filelist)
resolution_percentage = utils.calculate_resizing_tofitmemory(int(sx), int(sy), n_slices, bits/8)
if resolution_percentage < 1.0:
re_dialog = dialog.ResizeImageDialog()
re_dialog.SetValue(int(resolution_percentage*100))
re_dialog_value = re_dialog.ShowModal()
re_dialog.Close()
if re_dialog_value == wx.ID_OK:
percentage = re_dialog.GetValue()
resolution_percentage = percentage / 100.0
else:
return
xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
wl = float(dicom.image.level)
ww = float(dicom.image.window)
self.matrix, scalar_range, self.filename = image_utils.dcm2memmap(filelist, size,
orientation, resolution_percentage)
self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
self.Slice.matrix_filename = self.filename
if orientation == 'AXIAL':
self.Slice.spacing = xyspacing[0], xyspacing[1], zspacing
elif orientation == 'CORONAL':
self.Slice.spacing = xyspacing[0], zspacing, xyspacing[1]
elif orientation == 'SAGITTAL':
self.Slice.spacing = zspacing, xyspacing[1], xyspacing[0]
# 1(a): Fix gantry tilt, if any
tilt_value = dicom.acquisition.tilt
if (tilt_value) and (gui):
# Tell user gantry tilt and fix, according to answer
message = _("Fix gantry tilt applying the degrees below")
value = -1*tilt_value
tilt_value = dialog.ShowNumberDialog(message, value)
image_utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
elif (tilt_value) and not (gui):
tilt_value = -1*tilt_value
image_utils.FixGantryTilt(self.matrix, self.Slice.spacing, tilt_value)
self.Slice.window_level = wl
self.Slice.window_width = ww
scalar_range = int(self.matrix.min()), int(self.matrix.max())
Publisher.sendMessage('Update threshold limits list', scalar_range)
return self.matrix, self.filename, dicom
def OnPopup(self, evt):
id = evt.GetId()
item = self.ID_TO_TOOL_ITEM[evt.GetId()]
key = item.GetLabel()
if(key in const.WINDOW_LEVEL.keys()):
window, level = const.WINDOW_LEVEL[key]
Publisher.sendMessage('Bright and contrast adjustment image',
(window, level))
Publisher.sendMessage('Update window level value',\
(window, level))
Publisher.sendMessage('Update window and level text',\
"WL: %d WW: %d"%(level, window))
Publisher.sendMessage('Update slice viewer')
#Necessary update the slice plane in the volume case exists
Publisher.sendMessage('Render volume viewer')
elif(key in const.SLICE_COLOR_TABLE.keys()):
values = const.SLICE_COLOR_TABLE[key]
Publisher.sendMessage('Change colour table from background image', values)
Publisher.sendMessage('Update slice viewer')
if sys.platform == 'linux2':
for i in self.pseudo_color_items:
it = self.pseudo_color_items[i]
if it.IsChecked():
it.Toggle()
item.Toggle()
self.HideClutDialog()
self._gen_event = True
elif key in self.plist_presets:
values = presets.get_wwwl_preset_colours(self.plist_presets[key])
Publisher.sendMessage('Change colour table from background image from plist', values)
Publisher.sendMessage('Update slice viewer')
if sys.platform == 'linux2':
for i in self.pseudo_color_items:
it = self.pseudo_color_items[i]
if it.IsChecked():
it.Toggle()
item.Toggle()
self.HideClutDialog()
self._gen_event = True
elif(key in const.IMAGE_TILING.keys()):
values = const.IMAGE_TILING[key]
Publisher.sendMessage('Set slice viewer layout', values)
Publisher.sendMessage('Update slice viewer')
elif key in PROJECTIONS_ID:
pid = PROJECTIONS_ID[key]
Publisher.sendMessage('Set projection type', pid)
Publisher.sendMessage('Reload actual slice')
elif key == _('Custom'):
if self.cdialog is None:
slc = sl.Slice()
histogram = slc.histogram
init = slc.matrix.min()
end = slc.matrix.max()
nodes = slc.nodes
self.cdialog = ClutImagedataDialog(histogram, init, end, nodes)
self.cdialog.Show()
else:
self.cdialog.Show(self._gen_event)
if sys.platform == 'linux2':
for i in self.pseudo_color_items:
it = self.pseudo_color_items[i]
if it.IsChecked():
it.Toggle()
item.Toggle()
item = self.ID_TO_TOOL_ITEM[evt.GetId()]
item.Check(True)
self._gen_event = False
evt.Skip()
