def UpdateThresholdModes(self, threshold_range):
thresh_min, thresh_max = threshold_range
presets_list = (self.thresh_ct, self.thresh_mri)
for presets in presets_list:
for key in presets:
(t_min, t_max) = presets[key]
print(key, t_min, t_max)
if (t_min is None) or (t_max is None): # setting custom preset
t_min = thresh_min
t_max = thresh_max
if (t_min < thresh_min):
t_min = thresh_min
if (t_max > thresh_max):
t_max = thresh_max
# This has happened in Analyze files
# TODO: find a good solution for presets in Analyze files
if (t_min > thresh_max):
t_min = thresh_min
if (t_max < thresh_min):
t_max = thresh_max
presets[key] = (t_min, t_max)
Publisher.sendMessage('Update threshold limits',
threshold_range=(thresh_min, thresh_max))
def ReadBitmap(filepath):
t = VerifyDataType(filepath)
if _has_win32api:
filepath = win32api.GetShortPathName(filepath)
if t == False:
try:
measures_info = GetPixelSpacingFromInfoFile(filepath)
except UnicodeDecodeError:
measures_info = False
if measures_info:
Publisher.sendMessage("Set bitmap spacing", spacing=measures_info)
return False
img_array = VtkRead(filepath, t)
if not (isinstance(img_array, numpy.ndarray)):
no_error = True
img_array = ScipyRead(filepath)
if not (isinstance(img_array, numpy.ndarray)):
return False
return img_array
def OnComboBrushOp(self, evt):
brush_op_id = evt.GetSelection()
Publisher.sendMessage('Set edition operation', operation=brush_op_id)
if brush_op_id == const.BRUSH_THRESH:
self.gradient_thresh.Enable()
else:
self.gradient_thresh.Disable()
def OnRemove(self, surface_indexes):
proj = prj.Project()
old_dict = self.actors_dict
new_dict = {}
if surface_indexes:
for index in surface_indexes:
proj.RemoveSurface(index)
if index in old_dict:
actor = old_dict[index]
for i in old_dict:
if i < index:
new_dict[i] = old_dict[i]
if i > index:
new_dict[i - 1] = old_dict[i]
old_dict = new_dict
Publisher.sendMessage('Remove surface actor from viewer',
actor=actor)
self.actors_dict = new_dict
if self.last_surface_index in surface_indexes:
if self.actors_dict:
self.last_surface_index = 0
else:
self.last_surface_index = None
def OnSlideChanging(self, evt):
thresh_min = self.gradient.GetMinValue()
thresh_max = self.gradient.GetMaxValue()
Publisher.sendMessage('Changing threshold values',
threshold_range=(thresh_min, thresh_max))
session = ses.Session()
session.ChangeProject()
def OnBrushSize(self, evt):
""" """
# FIXME: Using wx.EVT_SPINCTRL in MacOS it doesnt capture changes only
# in the text ctrl - so we are capturing only changes on text
# Strangelly this is being called twice
Publisher.sendMessage('Set edition brush size',
size=self.spin.GetValue())
def OnLinkNewMask(self, evt=None):
try:
evt.data
evt = None
except:
pass
dialog = dlg.NewMask()
try:
if dialog.ShowModal() == wx.ID_OK:
ok = 1
else:
ok = 0
except (wx._core.PyAssertionError): #TODO FIX: win64
ok = 1
if ok:
mask_name, thresh, colour = dialog.GetValue()
if mask_name:
Publisher.sendMessage('Create new mask',
mask_name=mask_name,
thresh=thresh,
colour=colour)
dialog.Destroy()
def OnFoldPressCaption(self, evt):
id = evt.GetTag().GetId()
closed = evt.GetFoldStatus()
if self.__id_editor == id:
if closed:
Publisher.sendMessage('Disable style',
style=const.SLICE_STATE_EDITOR)
self.last_style = None
else:
Publisher.sendMessage('Enable style',
style=const.SLICE_STATE_EDITOR)
self.last_style = const.SLICE_STATE_EDITOR
elif self.__id_watershed == id:
if closed:
Publisher.sendMessage('Disable style',
style=const.SLICE_STATE_WATERSHED)
self.last_style = None
else:
Publisher.sendMessage('Enable style',
style=const.SLICE_STATE_WATERSHED)
# Publisher.sendMessage('Show help message', 'Mark the object and the background')
self.last_style = const.SLICE_STATE_WATERSHED
else:
Publisher.sendMessage('Disable style',
style=const.SLICE_STATE_EDITOR)
self.last_style = None
evt.Skip()
wx.CallAfter(self.ResizeFPB)
def OnLinkExportMask(self, evt=None):
project = proj.Project()
if sys.platform == 'win32':
project_name = project.name
else:
project_name = project.name + ".vti"
dlg = wx.FileDialog(
None,
"Save mask as...", # title
"", # last used directory
project_name, # filename
WILDCARD_SAVE_MASK,
wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
dlg.SetFilterIndex(0) # default is VTI
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
extension = "vti"
if sys.platform != 'win32':
if filename.split(".")[-1] != extension:
filename = filename + "." + extension
filetype = const.FILETYPE_IMAGEDATA
Publisher.sendMessage('Export mask to file',
filename=filename,
filetype=filetype)
def __init__(self, size=50):
self.history = []
self.index = -1
self.size = size * 2
Publisher.sendMessage("Enable undo", value=False)
Publisher.sendMessage("Enable redo", value=False)
def on_show(self):
self.history._config_undo_redo(self.is_shown)
if ses.Session().mask_3d_preview:
Publisher.sendMessage('Show mask preview',
index=self.index,
flag=bool(self.is_shown))
Publisher.sendMessage("Render volume viewer")
def UpdateSurfaceInterpolation(self):
interpolation = int(ses.Session().surface_interpolation)
key_actors = self.actors_dict.keys()
for key in self.actors_dict:
self.actors_dict[key].GetProperty().SetInterpolation(interpolation)
Publisher.sendMessage('Render volume viewer')
def OnMenuView(self, evt):
"""Events from button menus."""
bmp = wx.Bitmap(ID_TO_BMP[evt.GetId()][1], wx.BITMAP_TYPE_PNG)
self.button_view.SetBitmapSelected(bmp)
Publisher.sendMessage('Set volume view angle', view=evt.GetId())
self.Refresh()
def OnSetRelativeWindowLevel(self, diff_wl, diff_ww):
ww = self.ww + diff_ww
wl = self.wl + diff_wl
Publisher.sendMessage('Set volume window and level text', ww=ww, wl=wl)
self.SetWWWL(ww, wl)
self.ww = ww
self.wl = wl
def OnEditLabel(self, evt):
if not evt.IsEditCancelled():
index = evt.GetIndex()
self.SetItem(index, 1, evt.GetLabel())
Publisher.sendMessage('Change mask name',
index=evt.GetIndex(), name=evt.GetLabel())
evt.Skip()
def _midi_to_pedal(self, msg):
# TODO: At this stage, interpret all note_on messages as the pedal being pressed,
# and note_off messages as the pedal being released. Later, use the correct
# message types and be more stringent about the messages.
#
if msg.type == 'note_on':
state = True
elif msg.type == 'note_off':
state = False
else:
print("Unknown message type received from MIDI device")
return
Publisher.sendMessage('Pedal state changed', state=state)
for callback_info in self._callback_infos:
callback = callback_info['callback']
callback(state)
if not state:
self._callback_infos = [
callback_info for callback_info in self._callback_infos
if not callback_info['remove_when_released']
]
def CleanUp(self):
Publisher.sendMessage('Toggle toolbar item',
_id=self.state_code,
value=False)
self.viewer.on_wl = True
self.viewer.text.Hide()
self.viewer.interactor.Render()
def ImportMedicalImages(self, directory, gui=True):
patients_groups = dcm.GetDicomGroups(directory)
name = directory.rpartition('\\')[-1].split('.')
if len(patients_groups):
# OPTION 1: DICOM
group = dcm.SelectLargerDicomGroup(patients_groups)
matrix, matrix_filename, dicom = self.OpenDicomGroup(group,
0, [0, 0],
gui=gui)
if matrix is None:
return
self.CreateDicomProject(dicom, matrix, matrix_filename)
else:
# OPTION 2: NIfTI, Analyze or PAR/REC
if name[-1] == 'gz':
name[1] = 'nii.gz'
suptype = ('hdr', 'nii', 'nii.gz', 'par')
filetype = name[1].lower()
if filetype in suptype:
group = oth.ReadOthers(directory)
else:
utils.debug("No medical images found on given directory")
return
if group:
matrix, matrix_filename = self.OpenOtherFiles(group)
self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
# OPTION 4: Nothing...
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
def OpenBitmapFiles(self, bmp_data, rec_data):
name = rec_data[0]
orientation = rec_data[1]
sp_x = float(rec_data[2])
sp_y = float(rec_data[3])
sp_z = float(rec_data[4])
interval = int(rec_data[5])
interval += 1
filelist = bmp_data.GetOnlyBitmapPath()[::interval]
bits = bmp_data.GetFirstPixelSize()
sx, sy = size = bmp_data.GetFirstBitmapSize()
n_slices = len(filelist)
resolution_percentage = utils.calculate_resizing_tofitmemory(
int(sx), int(sy), n_slices, bits / 8)
zspacing = sp_z * interval
xyspacing = (sp_y, sp_x)
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
self.matrix, scalar_range, self.filename = image_utils.bitmap2memmap(
filelist, size, orientation, (sp_z, sp_y, sp_x),
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]
self.Slice.window_level = float(self.matrix.max() / 4)
self.Slice.window_width = float(self.matrix.max())
scalar_range = int(self.matrix.min()), int(self.matrix.max())
Publisher.sendMessage('Update threshold limits list',
threshold_range=scalar_range)
return self.matrix, self.filename #, dicom
def disable_mask_preview(self):
ses.Session().mask_3d_preview = False
mask = self.Slice.current_mask
if mask is not None:
Publisher.sendMessage("Remove mask preview",
mask_3d_actor=mask.volume._actor)
Publisher.sendMessage("Render volume viewer")
def SaveProject(self, path=None, compress=False):
Publisher.sendMessage('Begin busy cursor')
session = ses.Session()
if path:
dirpath, filename = os.path.split(path)
else:
dirpath, filename = session.project_path
if isinstance(filename, str):
filename = utils.decode(filename, const.FS_ENCODE)
proj = prj.Project()
try:
prj.Project().SavePlistProject(dirpath, filename, compress)
except PermissionError as err:
if wx.GetApp() is None:
print(
"Error: Permission denied, you don't have permission to write at {}"
.format(dirpath))
else:
dlg = dialogs.ErrorMessageBox(
None, "Save project error",
"It was not possible to save because you don't have permission to write at {}\n{}"
.format(dirpath, err))
dlg.ShowModal()
dlg.Destroy()
else:
session.SaveProject((dirpath, filename))
Publisher.sendMessage('End busy cursor')
def OnDuplicate(self):
selected_items = self.parent.listctrl.GetSelected()
if selected_items:
Publisher.sendMessage('Duplicate surfaces',
surface_indexes=selected_items)
else:
dlg.SurfaceSelectionRequiredForDuplication()
def OnDuplicate(self):
selected_items = self.parent.listctrl.GetSelected()
if selected_items:
Publisher.sendMessage('Duplicate masks',
mask_indexes=selected_items)
else:
dlg.MaskSelectionRequiredForDuplication()
def RemoveMeasurements(self):
"""
Remove items selected.
"""
# it is necessary to update internal dictionary
# that maps bitmap given item index
selected_items = self.GetSelected()
selected_items.sort(reverse=True)
old_dict = self._list_index
if selected_items:
for index in selected_items:
new_dict = {}
self.DeleteItem(index)
for i in old_dict:
if i < index:
new_dict[i] = old_dict[i]
if i > index:
new_dict[i - 1] = old_dict[i]
old_dict = new_dict
self._list_index = new_dict
Publisher.sendMessage('Remove measurements',
indexes=selected_items)
else:
dlg.MeasureSelectionRequiredForRemoval()
def StopNavigation(self):
self.event.set()
if self.pedal_connection is not None:
self.pedal_connection.remove_callback(name='navigation')
self.coord_queue.clear()
self.coord_queue.join()
if self.serial_port_connection is not None:
self.serial_port_connection.join()
if self.serial_port_in_use:
self.serial_port_queue.clear()
self.serial_port_queue.join()
if self.view_tracts:
self.coord_tracts_queue.clear()
self.coord_tracts_queue.join()
self.tracts_queue.clear()
self.tracts_queue.join()
vis_components = [
self.serial_port_in_use, self.view_tracts, self.peel_loaded
]
Publisher.sendMessage("Navigation status",
nav_status=False,
vis_status=vis_components)
def find_plugins(self):
self.plugins = {}
for p in chain(
glob.glob(str(
inv_paths.PLUGIN_DIRECTORY.joinpath("**/plugin.json")),
recursive=True),
glob.glob(str(
inv_paths.USER_PLUGINS_DIRECTORY.joinpath(
"**/plugin.json")),
recursive=True),
):
try:
p = pathlib.Path(p)
with p.open() as f:
jdict = json.load(f)
plugin_name = jdict["name"]
plugin_description = jdict["description"]
enable_startup = jdict.get("enable-startup", False)
self.plugins[plugin_name] = {
"name": plugin_name,
"description": plugin_description,
"folder": p.parent,
"enable_startup": enable_startup,
}
except Exception as err:
print("It was not possible to load plugin. Error: {}".format(
err))
Publisher.sendMessage("Add plugins menu items", items=self.plugins)
def SetUp(self):
Publisher.sendMessage('Toggle toolbar item',
_id=self.state_code,
value=True)
self.viewer.on_wl = True
if self.viewer.raycasting_volume:
self.viewer.text.Show()
self.viewer.interactor.Render()
def _check_disconnected(self):
if self._midi_in is not None:
if self._active_input not in self._midi_inputs:
self._midi_in = None
Publisher.sendMessage('Pedal connection', state=False)
print("Disconnected from MIDI device")
def OnOpenMesh(self):
filename = dlg.ShowImportMeshFilesDialog()
if filename:
if not np.allclose(slice_.Slice().affine, np.eye(4)):
convert_to_inv = dlg.ImportMeshCoordSystem()
Publisher.sendMessage('Update convert_to_inv flag',
convert_to_inv=convert_to_inv)
Publisher.sendMessage('Import surface file', filename=filename)
def SetActorColour(self, surface_index, colour):
"""
"""
self.actors_dict[surface_index].GetProperty().SetColor(colour[:3])
# Update value in project's surface_dict
proj = prj.Project()
proj.surface_dict[surface_index].colour = colour
Publisher.sendMessage('Render volume viewer')
