def import_dicom_directory(parent = None, dtype = numpy.single, recursive=False,
load_all_images=False):
""" Import an image from a directory containing DICOM files
parent : parent wx Window for dialogs
dtype : type to cast images to, or None to preserve original type
recursive : set to True to recursively search for DICOM files
load_all_images : load all images contained in a file or just the first one
"""
preferences = medipy.gui.base.Preferences(
wx.GetApp().GetAppName(), wx.GetApp().GetVendorName())
path = preferences.get("IO/load_path", "")
dialog = wx.DirDialog(parent, defaultPath=path, style=wx.FD_OPEN)
if dialog.ShowModal() != wx.ID_OK :
return []
files = []
if recursive :
for dirpath, dirnames, filenames in os.walk(dialog.GetPath()) :
files.extend(os.path.join(dirpath, x) for x in filenames)
else :
files = [x for x in glob.glob(os.path.join(dialog.GetPath(), "*"))
if os.path.isfile(x)]
def loader(files) :
datasets = []
for file in files :
if medipy.io.dicom.can_read(str(file)) :
datasets.append(medipy.io.dicom.read(str(file)))
return datasets
periodic_progress_dialog = PeriodicProgressDialog(
0.2, "Loading files", "Loading ...")
worker_thread = WorkerThread(periodic_progress_dialog,
target=loader, args=(files,))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
periodic_progress_dialog.Destroy()
images = reconstruction.images(worker_thread.result, parent, dtype)
if images :
preferences.set("IO/load_path", dialog.GetPath())
return images
else :
return []
def get_dl(self,connection,dummy):
""" Get SCU call, download selected objects
Return a list of DataSets
"""
periodic_progress_dialog = PeriodicProgressDialog(0.2, "Get Retrieve",
"Retrieving Data From Server ...")
get_query = self.GetSelectedUids()
results=[]
for query in get_query:
query_level = self.GetQueryLevel(query)
get = medipy.network.dicom.scu.Get(connection, "patient", query_level, query)
worker_thread = WorkerThread(periodic_progress_dialog,target=get)
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
results.extend(worker_thread.result)
periodic_progress_dialog.Destroy()
return results
def move_dl(self,connection,destination):
""" Move SCU call to send selected objects to specified desination
Return a list of DataSets
"""
periodic_progress_dialog = PeriodicProgressDialog(0.2, "Move Retrieve",
"Retrieving Data From Server ...")
move_query = self.GetSelectedUids()
results = []
for query in move_query:
query_level = self.GetQueryLevel(query)
move = medipy.network.dicom.scu.Move(connection, "patient", query_level,
destination, query)
worker_thread = WorkerThread(periodic_progress_dialog,target=move)
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
results.extend(worker_thread.result)
periodic_progress_dialog.Destroy()
return results
def save(image, parent=None):
""" Save an image with appropriate dialogs (file selector)
Return the chosen save path or None
parent : parent wx Window for dialogs
"""
dialog = ImageFileDialog(parent, style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dialog.ShowModal() != wx.ID_OK :
return None
path = dialog.GetPath()
if isinstance(image, list) :
periodic_progress_dialog = PeriodicProgressDialog(0.2, "Saving files", "Saving ...")
worker_thread = WorkerThread(periodic_progress_dialog,target=medipy.io.save_serie, args=(image,path,))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
periodic_progress_dialog.Destroy()
else :
try :
medipy.io.save(image, path)
return path
except :
# Try by adding a ".nii" suffix
try :
path += ".nii"
medipy.io.save(image, path)
return path
except :
exc_info = sys.exc_info()
logging.error("".join(traceback.format_exception(*exc_info)))
wx.MessageBox("Could not save image to %s: %s"%(path, exc_info[1]),
"Could not save image", wx.OK|wx.ICON_ERROR)
def __call__(self):
# Save the current value of the parameters
# self._save_parameters()
# Build the expression namespace
namespace = {"function": self._function}
for parameter in self._parameters:
if parameter.get("role", "") == "return":
namespace[parameter["name"]] = None
elif parameter.get("role", "") == "output":
# Special case for images and 3D viewers
if parameter["type"] == "Image" and self._controls[
parameter["name"]].output_checked:
dummy = Image(shape=(1, 1, 1), value=0, dtype=numpy.single)
namespace[parameter["name"]] = dummy
elif parameter["type"] == "Object3D":
dummy = Object3D(name="New object")
namespace[parameter["name"]] = dummy
else:
namespace[parameter["name"]] = self._controls[
parameter["name"]].value
else:
# Parameter will not be modified
namespace[parameter["name"]] = self._controls[
parameter["name"]].value
# Build the expression
args = []
return_values = []
for parameter in self._parameters:
if parameter.get("role", "") == "return":
return_values.append(parameter["name"])
else:
args.append("{0} = {0}".format(parameter["name"]))
expression = "function({0})".format(", ".join(args))
if return_values:
return_expression = ", ".join(return_values)
expression = "{0} = {1}".format(return_expression, expression)
# Execute it
def f():
exec expression in namespace
periodic_progress_dialog = PeriodicProgressDialog(
0.2, "Running %s ..." % self._function.func_name,
"Running %s ..." % self._function.func_name)
worker_thread = WorkerThread(periodic_progress_dialog, target=f)
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
periodic_progress_dialog.Destroy()
if worker_thread.exception:
wx.MessageBox(
"Could not run function : {0}".format(worker_thread.exception),
"Could not run function")
else:
# Update controls and application
for parameter in self._parameters:
if parameter.get("role", "") not in ["return", "output"]:
# Parameter has not been modified
continue
else:
name = parameter["name"]
value = namespace[name]
control = self._controls[name]
# Special case for Image and Object3D
if parameter["type"] == "Image":
if control.output_checked:
self.notify_observers("new_image", image=value)
else:
self.notify_observers("replace_image",
old=control.value,
new=value)
elif parameter["type"] == "Object3D":
if control.output_checked:
viewer = Viewer3DFrame(parent=None,
objects_3d=ObservableList())
viewer.Show()
self.notify_observers("new_viewer_3d",
viewer=viewer)
control.value = self._viewer_3ds[-1]
viewer_3d = control.value
viewer_3d.objects_3d.append(value)
# If object has an associated image, set the GUI image
image = value.image
if image is not None:
self.notify_observers("set_image_to_object_3d",
image=image,
object_3d=value)
if len(viewer_3d.objects_3d) == 1:
viewer_3d.view_all()
viewer_3d.update_object_editor()
# In any case but Object3D (whose value is a Viewer3D),
# update the control
if parameter["type"] != "Object3D":
control.value = value
def load(parent=None, dtype=numpy.single, multiple=False, wildcard="*"):
""" Load images with appropriate dialogs (file selector, and DICOM selector
if needed).
parent : parent wx Window for dialogs
dtype : type to cast images to, or None to preserve original type
multiple : allow selection of several images
wildcard : dialog wildcard
Return a list of loaded images
"""
style = (wx.FD_OPEN | wx.FD_MULTIPLE) if multiple else wx.FD_OPEN
dialog = ImageFileDialog(parent, style=style)
dialog.SetWildcard(wildcard)
if dialog.ShowModal() != wx.ID_OK :
return []
paths = dialog.GetPaths() if multiple else [dialog.GetPath()]
images = []
dicomdirs, non_dicomdirs = _separate_dicomdirs(paths)
# Load all dicomdirs
for path in dicomdirs :
periodic_progress_dialog = PeriodicProgressDialog(
0.2, "Loading DICOMDIR", "Loading ...")
worker_thread = WorkerThread(periodic_progress_dialog,
target=medipy.io.dicom.read,
args=(path,))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
periodic_progress_dialog.Destroy()
if worker_thread.exception is not None :
wx.MessageBox("Could not load file {0} : {1}".format(
path, worker_thread.exception), "Could not load DICOMDIR")
else :
new_images = reconstruction.images(
[worker_thread.result], parent, dtype)
if new_images:
images.append(new_images)
# Load other images
periodic_progress_dialog = PeriodicProgressDialog(0.2, "Loading image",
"Loading ...")
for path in non_dicomdirs :
periodic_progress_dialog.Pulse("Loading {0}...".format(path))
periodic_progress_dialog.Fit()
worker_thread = WorkerThread(periodic_progress_dialog,
target=medipy.io.load, args=(path, dtype))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
if worker_thread.exception is not None :
wx.MessageBox("Could not load file {0} : {1}".format(
path, worker_thread.exception), "Could not load image")
else :
if worker_thread.result:
images.append(worker_thread.result)
periodic_progress_dialog.Destroy()
return images
def images(datasets,
parent,
dtype=numpy.single,
size=(700, 700),
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER):
""" Return a list of medipy.base.Image objects from a list of DataSets.
"""
dialog = ExplorerDialog(parent, size=size, style=style)
dialog.set_datasets(datasets)
# Size must be specified explicitely on Windows
dialog.SetSize((700, 700))
if dialog.ShowModal() != wx.ID_OK:
dialog.Destroy()
return []
dialog.Destroy()
# Get selected series from dialog, load it.
series = dialog.get_selected_datasets()
periodic_progress_dialog = PeriodicProgressDialog(0.2, "Loading files",
"Loading files ...")
worker_thread = WorkerThread(periodic_progress_dialog,
target=medipy.io.dicom.load_dicomdir_records,
args=(series, ))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
periodic_progress_dialog.Destroy()
if worker_thread.exception is not None:
wx.MessageBox(
"Could not load series : %s" % (worker_thread.exception, ),
"Could not load series")
return []
series = worker_thread.result
# Reconstruct one image per stack
series = medipy.io.dicom.split.images(series)
series = medipy.io.dicom.normalize.normalize(series)
stacks = medipy.io.dicom.stacks(series)
result = []
periodic_progress_dialog = PeriodicProgressDialog(
0.2, "Reconstructing images",
"Reconstructing images (%i/%i) ..." % (0, len(stacks)))
for index, stack in enumerate(stacks):
periodic_progress_dialog.Pulse("Reconstructing images (%i/%i) ..." %
(index + 1, len(stacks)))
worker_thread = WorkerThread(periodic_progress_dialog,
target=medipy.io.dicom.image,
args=(stack, ))
worker_thread.start()
periodic_progress_dialog.start()
worker_thread.join()
if worker_thread.exception is not None:
wx.MessageBox(
"Could not reconstruct image : %s" %
(worker_thread.exception, ), "Could not reconstruct image")
else:
image = worker_thread.result
if dtype is not None:
image.data = image.data.astype(dtype)
result.append(image)
periodic_progress_dialog.Destroy()
return result