def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._reader = vtkgdcm.vtkGDCMImageReader()
# NB NB NB: for now we're SWITCHING off the VTK-compatible
# Y-flip, until the X-mirror issues can be solved.
self._reader.SetFileLowerLeft(1)
self._ici = vtk.vtkImageChangeInformation()
self._ici.SetInputConnection(0, self._reader.GetOutputPort(0))
# create output MedicalMetaData and populate it with the
# necessary bindings.
mmd = MedicalMetaData()
mmd.medical_image_properties = \
self._reader.GetMedicalImageProperties()
mmd.direction_cosines = \
self._reader.GetDirectionCosines()
self._output_mmd = mmd
module_utils.setup_vtk_object_progress(self, self._reader,
'Reading DICOM data')
self._view_frame = None
self._file_dialog = None
self._config.dicom_filenames = []
# if this is true, module will still try to load set even if
# IPP sorting fails by sorting images alphabetically
self._config.robust_spacing = False
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
class EditMedicalMetaData(IntrospectModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
def close(self):
IntrospectModuleMixin.close(self)
if self._view_frame is not None:
self._view_frame.Destroy()
ModuleBase.close(self)
def get_input_descriptions(self):
return ('Medical Meta Data', )
def set_input(self, idx, input_stream):
self._input_mmd = input_stream
def get_output_descriptions(self):
return ('Medical Meta Data', )
def get_output(self, idx):
return self._output_mmd
def execute_module(self):
# 1. if self._input_mmd is set, copy from self._input_mmd to
# self._output_mmd (mmd.deep_copy checks for None)
self._output_mmd.deep_copy(self._input_mmd)
# 2. show input_mmd.medical_image_properties values in the
# 'current values' column of the properties grid, only if this
# module's view has already been shown
self._grid_sync_with_current()
# 3. apply only changed fields from interface
mip = self._output_mmd.medical_image_properties
for key, val in self._config.new_value_dict.items():
getattr(mip, 'Set%s' % (key))(val)
def logic_to_config(self):
pass
def config_to_logic(self):
pass
def config_to_view(self):
if self._config.new_value_dict != self._grid_value_dict:
self._grid_value_dict.clear()
self._grid_value_dict.update(self._config.new_value_dict)
# now sync grid_value_dict to actual GUI
self._grid_sync_with_dict()
def view_to_config(self):
if self._config.new_value_dict == self._grid_value_dict:
# these two are still equal, so we don't have to do
# anything. Return False to indicate that nothing has
# changed.
return False
# transfer all values from grid_value_dict to dict in config
self._config.new_value_dict.clear()
self._config.new_value_dict.update(self._grid_value_dict)
def view(self):
# all fields touched by user are recorded. when we get a new
# input, these fields are left untouched. mmmkay?
if self._view_frame is None:
self._create_view_frame()
self.sync_module_view_with_logic()
self._view_frame.Show(True)
self._view_frame.Raise()
def _create_view_frame(self):
import modules.filters.resources.python.EditMedicalMetaDataViewFrame
reload(modules.filters.resources.python.EditMedicalMetaDataViewFrame)
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
modules.filters.resources.python.EditMedicalMetaDataViewFrame.\
EditMedicalMetaDataViewFrame)
# resize the grid and populate it with the various property
# names
grid = self._view_frame.prop_grid
grid.DeleteRows(0, grid.GetNumberRows())
grid.AppendRows(len(self.mip_attr_l))
for i in range(len(self.mip_attr_l)):
grid.SetCellValue(i, 0, self.mip_attr_l[i])
# key is read-only
grid.SetReadOnly(i, 0)
# current value is also read-only
grid.SetReadOnly(i, 1)
# use special method to set new value (this also takes
# care of cell colouring)
self._grid_set_new_val(i, None)
# make sure the first column fits neatly around the largest
# key name
grid.AutoSizeColumn(0)
def handler_grid_cell_change(event):
# event is a wx.GridEvent
r, c = event.GetRow(), event.GetCol()
grid = self._view_frame.prop_grid
key = self.mip_attr_l[r]
gval = grid.GetCellValue(r, c)
if gval == '':
# this means the user doesn't want this field to be
# changed, so we have to remove it from the
# _grid_value_dict and we have to adapt the cell
del self._grid_value_dict[key]
# we only use this to change the cell background
self._grid_set_new_val(r, gval, value_change=False)
else:
# the user has changed the value, so set it in the
# prop dictionary
self._grid_value_dict[key] = gval
# and make sure the background colour is changed
# appropriately.
self._grid_set_new_val(r, gval, value_change=False)
grid.Bind(wx.grid.EVT_GRID_CELL_CHANGE, handler_grid_cell_change)
object_dict = {'Module (self)': self}
module_utils.create_standard_object_introspection(
self, self._view_frame, self._view_frame.view_frame_panel,
object_dict, None)
# we don't want enter to OK and escape to cancel, as these are
# used for confirming and cancelling grid editing operations
module_utils.create_eoca_buttons(self,
self._view_frame,
self._view_frame.view_frame_panel,
ok_default=False,
cancel_hotkey=False)
# follow ModuleBase convention to indicate that we now have
# a view
self.view_initialised = True
self._grid_sync_with_current()
def _grid_set_new_val(self, row, val, value_change=True):
grid = self._view_frame.prop_grid
if not val is None:
if value_change:
# this does not trigger the CELL_CHANGE handler
grid.SetCellValue(row, 2, val)
grid.SetCellBackgroundColour(row, 2, wx.WHITE)
else:
if value_change:
# this does not trigger the CELL_CHANGE handler
grid.SetCellValue(row, 2, '')
grid.SetCellBackgroundColour(row, 2, wx.LIGHT_GREY)
def _grid_sync_with_current(self):
"""If there's an input_mmd, read out all its data and populate
the current values column. This method is called by the
execute_data and also by _create_view_frame.
"""
# we only do this if we have a view
if not self.view_initialised:
return
if not self._input_mmd is None and \
self._input_mmd.__class__ == \
MedicalMetaData:
mip = self._input_mmd.medical_image_properties
grid = self._view_frame.prop_grid
for i in range(len(self.mip_attr_l)):
key = self.mip_attr_l[i]
val = getattr(mip, 'Get%s' % (key, ))()
if val == None:
val = ''
grid.SetCellValue(i, 1, val)
def _grid_sync_with_dict(self):
"""Synchronise property grid with _grid_value_dict ivar.
"""
for kidx in range(len(self.mip_attr_l)):
key = self.mip_attr_l[kidx]
val = self._grid_value_dict.get(key, None)
self._grid_set_new_val(kidx, val)
class EditMedicalMetaData(IntrospectModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
def close(self):
IntrospectModuleMixin.close(self)
if self._view_frame is not None:
self._view_frame.Destroy()
ModuleBase.close(self)
def get_input_descriptions(self):
return ('Medical Meta Data',)
def set_input(self, idx, input_stream):
self._input_mmd = input_stream
def get_output_descriptions(self):
return ('Medical Meta Data',)
def get_output(self, idx):
return self._output_mmd
def execute_module(self):
# 1. if self._input_mmd is set, copy from self._input_mmd to
# self._output_mmd (mmd.deep_copy checks for None)
self._output_mmd.deep_copy(self._input_mmd)
# 2. show input_mmd.medical_image_properties values in the
# 'current values' column of the properties grid, only if this
# module's view has already been shown
self._grid_sync_with_current()
# 3. apply only changed fields from interface
mip = self._output_mmd.medical_image_properties
for key,val in self._config.new_value_dict.items():
getattr(mip, 'Set%s' % (key))(val)
def logic_to_config(self):
pass
def config_to_logic(self):
pass
def config_to_view(self):
if self._config.new_value_dict != self._grid_value_dict:
self._grid_value_dict.clear()
self._grid_value_dict.update(self._config.new_value_dict)
# now sync grid_value_dict to actual GUI
self._grid_sync_with_dict()
def view_to_config(self):
if self._config.new_value_dict == self._grid_value_dict:
# these two are still equal, so we don't have to do
# anything. Return False to indicate that nothing has
# changed.
return False
# transfer all values from grid_value_dict to dict in config
self._config.new_value_dict.clear()
self._config.new_value_dict.update(self._grid_value_dict)
def view(self):
# all fields touched by user are recorded. when we get a new
# input, these fields are left untouched. mmmkay?
if self._view_frame is None:
self._create_view_frame()
self.sync_module_view_with_logic()
self._view_frame.Show(True)
self._view_frame.Raise()
def _create_view_frame(self):
import modules.filters.resources.python.EditMedicalMetaDataViewFrame
reload(modules.filters.resources.python.EditMedicalMetaDataViewFrame)
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
modules.filters.resources.python.EditMedicalMetaDataViewFrame.\
EditMedicalMetaDataViewFrame)
# resize the grid and populate it with the various property
# names
grid = self._view_frame.prop_grid
grid.DeleteRows(0, grid.GetNumberRows())
grid.AppendRows(len(self.mip_attr_l))
for i in range(len(self.mip_attr_l)):
grid.SetCellValue(i, 0, self.mip_attr_l[i])
# key is read-only
grid.SetReadOnly(i, 0)
# current value is also read-only
grid.SetReadOnly(i, 1)
# use special method to set new value (this also takes
# care of cell colouring)
self._grid_set_new_val(i, None)
# make sure the first column fits neatly around the largest
# key name
grid.AutoSizeColumn(0)
def handler_grid_cell_change(event):
# event is a wx.GridEvent
r,c = event.GetRow(), event.GetCol()
grid = self._view_frame.prop_grid
key = self.mip_attr_l[r]
gval = grid.GetCellValue(r,c)
if gval == '':
# this means the user doesn't want this field to be
# changed, so we have to remove it from the
# _grid_value_dict and we have to adapt the cell
del self._grid_value_dict[key]
# we only use this to change the cell background
self._grid_set_new_val(r, gval, value_change=False)
else:
# the user has changed the value, so set it in the
# prop dictionary
self._grid_value_dict[key] = gval
# and make sure the background colour is changed
# appropriately.
self._grid_set_new_val(r, gval, value_change=False)
grid.Bind(wx.grid.EVT_GRID_CELL_CHANGE, handler_grid_cell_change)
object_dict = {
'Module (self)' : self}
module_utils.create_standard_object_introspection(
self, self._view_frame, self._view_frame.view_frame_panel,
object_dict, None)
# we don't want enter to OK and escape to cancel, as these are
# used for confirming and cancelling grid editing operations
module_utils.create_eoca_buttons(self, self._view_frame,
self._view_frame.view_frame_panel,
ok_default=False,
cancel_hotkey=False)
# follow ModuleBase convention to indicate that we now have
# a view
self.view_initialised = True
self._grid_sync_with_current()
def _grid_set_new_val(self, row, val, value_change=True):
grid = self._view_frame.prop_grid
if not val is None:
if value_change:
# this does not trigger the CELL_CHANGE handler
grid.SetCellValue(row, 2, val)
grid.SetCellBackgroundColour(row, 2, wx.WHITE)
else:
if value_change:
# this does not trigger the CELL_CHANGE handler
grid.SetCellValue(row, 2, '')
grid.SetCellBackgroundColour(row, 2, wx.LIGHT_GREY)
def _grid_sync_with_current(self):
"""If there's an input_mmd, read out all its data and populate
the current values column. This method is called by the
execute_data and also by _create_view_frame.
"""
# we only do this if we have a view
if not self.view_initialised:
return
if not self._input_mmd is None and \
self._input_mmd.__class__ == \
MedicalMetaData:
mip = self._input_mmd.medical_image_properties
grid = self._view_frame.prop_grid
for i in range(len(self.mip_attr_l)):
key = self.mip_attr_l[i]
val = getattr(mip, 'Get%s' % (key,))()
if val == None:
val = ''
grid.SetCellValue(i, 1, val)
def _grid_sync_with_dict(self):
"""Synchronise property grid with _grid_value_dict ivar.
"""
for kidx in range(len(self.mip_attr_l)):
key = self.mip_attr_l[kidx]
val = self._grid_value_dict.get(key,None)
self._grid_set_new_val(kidx, val)
