preliminary segmentations

painter/src/convert_seg.py

@@ -56,6 +56,12 @@ def convert_seg_to_annot(seg):
     annot[1] = seg_fg
     return annot
 
+def convert_seg_to_fg_annot(seg):
+    seg_fg = seg > 0
+    annot = np.zeros([2] + list(seg.shape))
+    annot[1] = seg_fg
+    return annot
+
 class ConvertProgressWidget(BaseProgressWidget):
 
     def __init__(self):

painter/src/im_viewer.py

@@ -47,9 +47,11 @@ def __init__(self, parent, view_mode):
         self.seg_visible = False
         self.image_visible = True
         self.guide_image_visible = False
+        self.prelabel_visible = False
         self.outline_visible = False
         self.image_pixmap_holder = None
         self.guide_image_pixmap_holder = None
+        self.prelabel_pixmap_holder = None
         self.seg_pixmap_holder = None
         self.blank_pixmap = None
         self.black_pixmap = None
@@ -108,13 +110,15 @@ def init_ui(self):
         self.inner_layout.addWidget(self.graphics_view)
         if self.mode == 'axial':
             self.vis_widget = VisibilityWidget(QtWidgets.QVBoxLayout, self,
-                                               show_guide=hasattr(self.parent, 'guide_image_dir'))
+                                               show_guide=hasattr(self.parent, 'guide_image_dir'),
+                                               show_prelabel=hasattr(self.parent, 'prelabel_dir'))
             self.vis_widget.setMaximumWidth(200)
             # left, top, right, bottom
             self.bottom_bar_layout.setContentsMargins(20, 0, 20, 0)
         else:
             self.vis_widget = VisibilityWidget(QtWidgets.QHBoxLayout, self,
-                                               show_guide=hasattr(self.parent, 'guide_image_dir'))
+                                               show_guide=hasattr(self.parent, 'guide_image_dir'),
+                                               show_prelabel=hasattr(self.parent, 'prelabel_dir'))
 
             self.vis_widget.setMaximumWidth(500)
             # left, top, right, bottom
@@ -145,6 +149,12 @@ def im_checkbox_change(self, state):
         checked = (state == QtCore.Qt.Checked)
         if checked is not self.image_visible:
             self.show_hide_image()
+
+    def prelabel_checkbox_change(self, state):
+        """ set checkbox to specified state and update visibility if required """
+        checked = (state == QtCore.Qt.Checked)
+        if checked is not self.prelabel_visible:
+            self.show_hide_prelabel()
 
     def outline_checkbox_change(self, state):
         """ set checkbox to specified state and update visibility if required """
@@ -280,6 +290,18 @@ def show_hide_annot(self):
             self.annot_visible = True
         self.vis_widget.annot_checkbox.setChecked(self.annot_visible)
 
+    def show_hide_prelabel(self):
+        """ show or hide the preliminary labels.
+            Could be useful to use them as annotations, if they are good.
+        """
+        if self.prelabel_visible:
+            self.prelabel_pixmap_holder.setPixmap(self.blank_pixmap)
+            self.prelabel_visible = False
+        else:
+            self.prelabel_pixmap_holder.setPixmap(self.prelabel_pixmap)
+            self.prelabel_visible = True
+        self.vis_widget.prelabel_checkbox.setChecked(self.prelabel_visible)
+
     def show_hide_outline(self):
         """ show or hide the current outline.
             Could be useful to help inspect the
@@ -424,7 +446,22 @@ def update_seg_slice(self):
         if not self.seg_visible:
             self.seg_pixmap_holder.setPixmap(self.blank_pixmap)
 
+        if self.parent.prelabel_data is not None:
+            prelabel_slice = im_utils.get_slice(self.parent.prelabel_data,
+                                           self.slice_nav.slice_idx,
+                                           self.mode)
+            self.prelabel_pixmap = im_utils.seg_slice_to_pixmap(prelabel_slice)
+            self.scene.prelabel_pixmap = self.prelabel_pixmap
+
+            if self.prelabel_pixmap_holder:
+                self.prelabel_pixmap_holder.setPixmap(self.prelabel_pixmap)
+                self.scene.prelabel_pixmap = self.prelabel_pixmap
+            else:
+                self.prelabel_pixmap_holder = self.scene.addPixmap(self.prelabel_pixmap)
+            if not self.prelabel_visible:
+                self.prelabel_pixmap_holder.setPixmap(self.blank_pixmap)
 
+
     def update_cursor(self, ctrl_press=False):
         """ render cursor based on zoom level,
             brush color and brush size """

painter/src/menus.py

@@ -7,7 +7,7 @@
 from PyQt5 import QtGui
 from segment_folder import SegmentFolderWidget
 from segment import segment_full_image
-from convert_seg import ConvertSegWidget, convert_seg_to_annot
+from convert_seg import ConvertSegWidget, convert_seg_to_annot, convert_seg_to_fg_annot
 from assign_corrections import AssignCorrectionsWidget
 from extract_image_props import ExtractSegImagePropsWidget
 from compute_metrics import ExtractSegMetricsWidget
@@ -156,7 +156,7 @@ def add_help_menu(self,  menu_bar):
     help_menu.addAction(shortcut_btn)
 
 
-def add_extras_menu(main_window, menu_bar, project_open=False):
+def add_extras_menu(main_window, menu_bar, project_open=False, prelabels = False):
     extras_menu = menu_bar.addMenu('Extras')
 
     def show_conv_to_annot():
@@ -196,6 +196,22 @@ def show_assign_corrections():
 
 
     if project_open:
+        if prelabels:
+            conv_this_annot_btn = QtWidgets.QAction(QtGui.QIcon('missing.png'),
+                                'Convert preliminary labels to current annotation',
+                                 main_window)
+            def convert_prelabel():
+                main_window.annot_data = convert_seg_to_fg_annot(main_window.prelabel_data)
+                for v in main_window.viewers:
+                    v.update_image()
+                    v.update_cursor()
+                    # # hide the segmentation if we don't have it
+                    # if main_window.seg_data is None and v.seg_visible:
+                    #     # show seg in order to show the loading message
+                    #     v.show_hide_seg()
+            conv_this_annot_btn.triggered.connect(convert_prelabel)
+            extras_menu.addAction(conv_this_annot_btn)  
+
         extend_dataset_btn = QtWidgets.QAction(QtGui.QIcon('missing.png'), 'Extend dataset', main_window)
         def update_dataset_after_check():
             was_extended, file_names = check_extend_dataset(main_window,
@@ -296,6 +312,11 @@ def add_view_menu(window, im_viewer, menu_bar):
     toggle_guide_image_visibility_btn.triggered.connect(im_viewer.show_hide_guide_image)
     view_menu.addAction(toggle_guide_image_visibility_btn)
 
+    toggle_prelabel_visibility_btn = QtWidgets.QAction(QtGui.QIcon('missing.png'), 'Toggle guide image visibility', window)
+    toggle_prelabel_visibility_btn.setShortcut('D')
+    toggle_prelabel_visibility_btn.setStatusTip('Show or hide image')
+    toggle_prelabel_visibility_btn.triggered.connect(im_viewer.show_hide_prelabel)
+    view_menu.addAction(toggle_prelabel_visibility_btn)
 
     # toggle outline visibility
     toggle_outline_visibility_btn = QtWidgets.QAction(QtGui.QIcon('missing.png'),

painter/src/root_painter.py

@@ -79,6 +79,8 @@ def __init__(self, sync_dir, contrast_presets, server_ip=None, server_port=None)
         self.im_height = None
         self.annot_data = None
         self.seg_data = None
+        self.prelabel_data = None
+        self.prelabel_exists = False
 
         # for patch segment, useful for knowing how much annotation to send to the server.
         self.input_shape = (52, 228, 228)
@@ -146,6 +148,10 @@ def open_project(self, proj_file_path):
             self.seg_dir = self.proj_location / 'segmentations'
             self.log_dir = self.proj_location / 'logs'
 
+            if 'prelabel_dir' in settings:
+                self.prelabel_dir = self.proj_location / 'prelabel'
+                self.prelabel_exists = True
+
             self.train_seg_dirs = []
             self.train_annot_dirs = []
             self.val_annot_dirs = []
@@ -304,7 +310,15 @@ def update_annot_and_seg(self):
         else:
             # it should come later
             self.seg_data = None
-
+
+        if hasattr(self, 'prelabel_dir'):
+            prelabel_image_path = os.path.join(os.path.join(self.prelabel_dir, self.fname))
+            # and a guide image is available for the current image.
+            if os.path.isfile(prelabel_image_path):
+                self.prelabel_data = im_utils.load_image(prelabel_image_path)
+            else:
+                pass
+
         for v in self.viewers:
             v.update_image()
             v.update_cursor()
@@ -459,7 +473,7 @@ def init_missing_project_ui(self):
 
 
         menus.add_help_menu(self, menu_bar)
-        menus.add_extras_menu(self, menu_bar)
+        menus.add_extras_menu(self, menu_bar, prelabels=self.prelabel_exists)
         menus.add_measurements_menu(self, menu_bar)
 
         # Add project btns to open window (so it shows something useful)
@@ -750,7 +764,7 @@ def add_menu(self):
         if len(self.classes) > 1:
             menus.add_class_menu(self, self.menu_bar)
         menus.add_help_menu(self, self.menu_bar)
-        menus.add_extras_menu(self, menu_bar, project_open=True)
+        menus.add_extras_menu(self, menu_bar, project_open=True, prelabels=self.prelabel_exists)
         menus.add_measurements_menu(self, menu_bar)
 
 

painter/src/visibility_widget.py

@@ -21,11 +21,11 @@
 
 class VisibilityWidget(QtWidgets.QWidget):
 
-    def __init__(self, layout_class, parent, show_guide=False):
+    def __init__(self, layout_class, parent, show_guide=False, show_prelabel=False):
         super().__init__()
-        self.initUI(layout_class, parent, show_guide)
+        self.initUI(layout_class, parent, show_guide, show_prelabel)
 
-    def initUI(self, layout_class, parent, show_guide):
+    def initUI(self, layout_class, parent, show_guide, show_prelabel):
         # container goes full width to allow contents to be center aligned within it.
         widget = QtWidgets.QWidget()
         layout = QtWidgets.QHBoxLayout()
@@ -56,6 +56,13 @@ def initUI(self, layout_class, parent, show_guide):
             guide_image_checkbox.setChecked(False)
             self.guide_image_checkbox = guide_image_checkbox
             self.guide_image_checkbox.stateChanged.connect(parent.guide_checkbox_change)
+
+        if show_prelabel:
+            prelabel_checkbox = QtWidgets.QCheckBox("Preliminary labels (D)")
+            container_layout.addWidget(prelabel_checkbox)
+            prelabel_checkbox.setChecked(False)
+            self.prelabel_checkbox = prelabel_checkbox
+            self.prelabel_checkbox.stateChanged.connect(parent.prelabel_checkbox_change)
 
         seg_checkbox.setChecked(False)
         annot_checkbox.setChecked(True)