def _retrieve_instance_frames(args):
'''Retrieves frames for an individual instances and either
writes them to standard output or files on disk or displays them in a GUI
(depending on the requested content type).
Frames can only be saved and shown if they are retrieved using
image media types.
'''
client = DICOMwebClient(args.url,
username=args.username,
password=args.password,
ca_bundle=args.ca_bundle,
cert=args.cert)
pixel_data = client.retrieve_instance_frames(
args.study_instance_uid,
args.series_instance_uid,
args.sop_instance_uid,
args.frame_numbers,
media_types=args.media_types,
)
for i, data in enumerate(pixel_data):
if args.save or args.show:
try:
image = Image.open(BytesIO(data))
except Exception:
try:
import jpeg_ls
image = jpeg_ls.decode(np.fromstring(data, dtype=np.uint8))
except Exception:
raise IOError('Cannot load retrieved frame as an image.')
if args.save:
filename = (
'{sop_instance_uid}_{frame_number}.{extension}'.format(
sop_instance_uid=args.sop_instance_uid,
frame_number=args.frame_numbers[i],
extension=image.format.lower()))
filepath = os.path.join(args.output_dir, filename)
_save_image(image, filepath)
elif args.show:
_show_image(image)
else:
_print_pixel_data(data)
# sop_instance_uid='1.2.840.113704.7.1.0.192317454216202.1587243260.27398',
# )
# print('instance')
# print(instance)
# print()
# print("Writing test file")
# instance.save_as('teste-dicom-exame10')
# print("File saved.")
frames = client.retrieve_instance_frames(
study_instance_uid=
'1.2.840.113704.7.1.0.253219132234129147.1587168555.1281',
series_instance_uid=
'1.2.840.113704.7.32.004.7.1.0.253219132234129147.1587168635.3928',
sop_instance_uid='1.2.840.113704.7.1.0.192317454216202.1587243260.27398',
frame_numbers=[1],
media_types=('image/jpeg', ),
)
print('frames', len(frames))
# print(frames)
print()
out_f = 'teste-pac-server'
for i, frame in enumerate(frames):
filename = f"{out_f}/frame-{i}.jpeg"
with open(filename, 'wb') as outfile:
class DICOMWindow(Gtk.Window):
def __init__(self, title="DICOM Viewer"):
self.client = DICOMwebClient(
url='http://dev-demo.sectra.se',
qido_url_prefix='SectraQidoRs/mrnissuers/all',
wado_url_prefix='SectraWadoRs/mrnissuers/all',
stow_url_prefix='SectraStowRs/mrnissuers/all')
# construct top window
Gtk.Window.__init__(
self,
title=title,
vexpand=True,
hexpand=True,
border_width=0,
)
# create top grid
self.grid = Gtk.Grid(vexpand=True,
hexpand=True,
column_homogeneous=True,
row_homogeneous=True)
self.add(self.grid) # add it to parent window
# STUDIES
self.study_store = StudyStore(client=self.client)
self.current_study_filter = None
self.study_filter = self.study_store.filter_new()
self.study_filter.set_visible_func(self.study_view_filter_func)
self.study_view = Gtk.TreeView.new_with_model(self.study_filter)
self.study_view.connect("row-activated",
self.on_study_view_row_activated
) # upon double-click or return press
self.study_selection = self.study_view.get_selection()
self.study_selection.set_mode(Gtk.SelectionMode.MULTIPLE)
self.study_selection.connect("changed",
self.on_study_selection_changed)
for i, column_title in enumerate([
"Study UID",
"Study Name",
"Person Name",
"Study Date",
"Study Time",
]):
if i == 0:
continue #skip "Study UID"
renderer = Gtk.CellRendererText()
column = Gtk.TreeViewColumn(column_title, renderer, text=i)
column.set_sort_column_id(i) #trying to make columns sortable
self.study_view.append_column(column)
self.study_view_scroller = Gtk.ScrolledWindow(vexpand=True,
hexpand=True)
self.study_view_scroller.add(self.study_view)
self.grid.attach(self.study_view_scroller,
left=0,
top=0,
width=1,
height=1)
# SERIESES
self.series_store = SeriesStore(client=self.client)
self.current_series_filter = None
self.series_filter = self.series_store.filter_new()
self.series_filter.set_visible_func(self.series_view_filter_func)
self.series_view = Gtk.TreeView.new_with_model(self.series_filter)
self.series_view.connect("row-activated",
self.on_series_view_row_activated
) # upon double-click or return press
self.series_selection = self.series_view.get_selection()
self.series_selection.set_mode(Gtk.SelectionMode.MULTIPLE)
self.series_selection.connect("changed",
self.on_series_selection_changed)
for i, column_title in enumerate(["Series UID", "Series Modality"]):
if i == 0:
continue # skip "Series UID"
renderer = Gtk.CellRendererText()
column = Gtk.TreeViewColumn(column_title, renderer, text=i)
self.series_view.append_column(column)
self.series_view_scroller = Gtk.ScrolledWindow(vexpand=True,
hexpand=True)
self.series_view_scroller.add(self.series_view)
self.grid.attach(self.series_view_scroller,
left=1,
top=0,
width=1,
height=1)
# INSTANCES
self.instance_store = InstanceStore(client=self.client)
self.current_instance_filter = None
self.instance_filter = self.instance_store.filter_new()
self.instance_filter.set_visible_func(self.instance_view_filter_func)
self.instance_view = Gtk.TreeView.new_with_model(self.instance_filter)
self.instance_view.connect("row-activated",
self.on_instance_view_row_activated
) # upon double-click or return press
self.instance_selection = self.instance_view.get_selection()
self.instance_selection.set_mode(Gtk.SelectionMode.MULTIPLE)
self.instance_selection.connect("changed",
self.on_instance_selection_changed)
for i, column_title in enumerate(["SOP Instance UID", "SOP Class"]):
if i == 0:
continue # skip "SOP Instance UID"
renderer = Gtk.CellRendererText()
column = Gtk.TreeViewColumn(column_title, renderer, text=i)
self.instance_view.append_column(column)
self.instance_view_scroller = Gtk.ScrolledWindow(vexpand=True,
hexpand=True)
self.instance_view_scroller.add(self.instance_view)
self.grid.attach(self.instance_view_scroller,
left=2,
top=0,
width=1,
height=1)
self.image_view = Gtk.Image()
self.image_view_scroller = Gtk.ScrolledWindow(vexpand=True,
hexpand=True)
self.image_view_scroller.add(self.image_view)
self.grid.attach(self.image_view_scroller,
left=0,
top=1,
width=3,
height=3)
self.show_all()
def on_study_view_row_activated(self, view, row_index, column):
print("on_study_view_row_activated:", view, " row_index:", row_index)
# clear in reverse order
self.clear_current_image_and_pixel_data()
self.clear_current_instance_store_and_view()
self.clear_current_series_store_and_view()
model, treeiter = view.get_selection().get_selected_rows()
self.study_instance_uid = model[row_index][0]
self.series_store.update_using_study(
study_instance_uid=self.study_instance_uid)
def on_study_selection_changed(self, selection):
# clear in reverse order
self.clear_current_image_and_pixel_data()
self.clear_current_instance_store_and_view()
self.clear_current_series_store_and_view()
# print('on_study_selection_changed: seletion:{}, selection_count={}'.format(selection,
# selection.count_selected_rows()))
# TODO visually present:
# study_metadata = self.client.retrieve_study_metadata(self.study_instance_uid)
def on_series_view_row_activated(self, view, row_index, column):
print("on_series_view_row_activated:", view, " row_index:", row_index)
# clear in reverse order
self.clear_current_image_and_pixel_data()
self.clear_current_instance_store_and_view()
model, treeiter = view.get_selection().get_selected_rows()
self.series_instance_uid = model[row_index][0]
self.instance_store.update_using_study_and_series(
study_instance_uid=self.study_instance_uid,
series_instance_uid=self.series_instance_uid)
def on_series_selection_changed(self, selection):
'''This is function is called too often so we cannot do any heavy work here.'''
# print('on_series_selection_changed: seletion:{}, selection_count={}'.format(selection,
# selection.count_selected_rows()))
# clear in reverse order
self.clear_current_image_and_pixel_data()
self.clear_current_instance_store_and_view()
# TODO visually present:
# series_metadata = self.client.retrieve_series_metadata(self.series_instance_uid)
def on_instance_view_row_activated(self, view, row_index, column):
print("on_instance_view_row_activated:", view, " row_index:",
row_index)
# clear in reverse order
self.clear_current_image_and_pixel_data()
model, treeiter = view.get_selection().get_selected_rows()
self.sop_instance_uid = model[row_index][0]
if True:
# TODO visually present more parts of:
instance_metadata = self.client.retrieve_instance_metadata(
study_instance_uid=self.study_instance_uid,
series_instance_uid=self.series_instance_uid,
sop_instance_uid=self.sop_instance_uid)[0]
self.image_height = try_get_attr(instance_metadata,
'00280010') # rows
self.image_width = try_get_attr(instance_metadata,
'00280011') # columns
self.image_bits_per_pixel = try_get_attr(
instance_metadata, '00280100') # bits per pixel
self.frame_count = try_get_attr(
instance_metadata, '00280008', '1'
) # only present for multi-frame image instances so default to 1
transfer_syntax_uid = try_get_attr(instance_metadata, '00020010')
if transfer_syntax_uid is not None:
transfer_type = DICOM_TRANSFER_SYNTAXES[transfer_syntax_uid]
image_format = None # possible values are None (uncompressed/raw), 'jpeg', or 'jp2'
try:
start = time.time()
frames = self.client.retrieve_instance_frames(
study_instance_uid=self.study_instance_uid,
series_instance_uid=self.series_instance_uid,
sop_instance_uid=self.sop_instance_uid,
frame_numbers=[1],
image_format=image_format)
stop = time.time()
print("Retrieving frame took {}".format(stop - start))
except requests.exceptions.HTTPError:
frames = [] # no frames
pass
# need to store frames because Pixbuf.new_from_data doesn't keep own
# reference to data so Python will destroy it without Gtk knowing about it
self.rgb_frames = len(frames) * [None]
for image_index, frame in enumerate(frames):
pixel_count = (self.image_width * self.image_height)
rgb_frame_temp = bytearray(
3 * pixel_count) # pre-allocate RGB pixels
if image_format is None: # raw pixels
start = time.time()
if self.image_bits_per_pixel == 8:
for j in range(0, pixel_count):
grey8 = frame[j]
rgb_frame_temp[3 * j + 0] = grey8
rgb_frame_temp[3 * j + 1] = grey8
rgb_frame_temp[3 * j + 2] = grey8
if self.image_bits_per_pixel == 16:
for j in range(0, pixel_count):
# 16-bit grey pixel value
grey16 = (256 * frame[2 * j + 1] +
frame[2 * j + 0])
grey8 = int(grey16 /
128) # 16-bit to 8-bit conversion
rgb_frame_temp[3 * j + 0] = grey8
rgb_frame_temp[3 * j + 1] = grey8
rgb_frame_temp[3 * j + 2] = grey8
else:
raise Exception("Cannot handle bits_per_pixel being" +
str(self.image_bits_per_pixel))
stop = time.time()
print("Converting frame to grey-scale RGB-image took {}".
format(stop - start))
# Ref: https://lazka.github.io/pgi-docs/#GdkPixbuf-2.0/classes/Pixbuf.html#GdkPixbuf.Pixbuf.new_from_data
# this better than `Pixbuf.new_from_bytes` which requires
# the data parameter to be wrapped in a GLib.Bytes object
# WARNING: be aware of that `new_from_data` is buggy. See for instance:
# https://stackoverflow.com/questions/29501835/gtk3-gdk-pixbuf-new-from-data-gives-segmentation-fault-core-dumped-error-13
start = time.time()
self.rgb_frames[image_index] = bytes(
rgb_frame_temp
) # bytearray needs to be wrapped in a `bytes` and store here in order to enot loose ref
pixbuf = Pixbuf.new_from_data(
self.rgb_frames[image_index], # data
Colorspace.RGB, # colorspace
False, # has_alpha
8, # bits_per_sample
self.image_width, # width
self.image_height, # height
self.image_width *
3, # rowstride, 3 because RGB has 3 bytes per pixel
None,
None) # rely on Python for deallocation
if image_index == 0:
self.image_view.set_from_pixbuf(pixbuf)
stop = time.time()
print("Display image took {}".format(stop - start))
elif image_format == 'jp2':
print("TODO Decode jp2 image...")
if False:
input_stream = Gio.MemoryInputStream.new_from_data(
frame, None)
pixbuf = Pixbuf.new_from_stream(input_stream, None)
if image_index == 0:
self.image_view.set_from_pixbuf(pixbuf)
def on_instance_selection_changed(self, selection):
'''This is function is called too often so we cannot do any heavy work here.'''
pass
# print('on_instance_selection_changed: seletion:{}, selection_count={}'.format(selection,
# selection.count_selected_rows()))
# TODO visually present:
# instance_metadata = self.client.retrieve_instance_metadata(self.instance_instance_uid)
def clear_current_series_store_and_view(self):
self.series_view.get_selection().unselect_all()
self.series_store.clear()
def clear_current_instance_store_and_view(self):
self.instance_view.get_selection().unselect_all()
self.instance_store.clear()
def clear_current_image_and_pixel_data(self):
self.image_view.clear() # remove image before
self.rgb_frames = None # drop pixel data
def study_view_filter_func(self, model, iter, data):
return True # accept everything for now
def series_view_filter_func(self, model, iter, data):
return True # accept everything for now
def instance_view_filter_func(self, model, iter, data):
return True # accept everything for now