Bug fix and various improvements (#1571)

* BUG: label_vertebrae: Updated label disc value (fixes #1570)

* REF: fixed typo

* OPT: label_vertebrae: Added instructions above image for sagittal dialog (fixes #1563)

scripts/sct_label_vertebrae.py

@@ -434,6 +434,7 @@ def vertebral_detection(fname, fname_seg, contrast, param, init_disc, verbose=1,
     # define mean distance (in voxel) between adjacent discs: [C1/C2 -> C2/C3], [C2/C3 -> C4/C5], ..., [L1/L2 -> L2/L3]
     centerline_level = data_disc_template[xct, yct, :]
     # attribute value to each disc. Starts from max level, then decrease.
+    # NB: value 2 means disc C2/C3 (and so on and so forth).
     min_level = centerline_level[centerline_level.nonzero()].min()
     max_level = centerline_level[centerline_level.nonzero()].max()
     list_disc_value_template = range(min_level, max_level)
@@ -469,15 +470,16 @@ def vertebral_detection(fname, fname_seg, contrast, param, init_disc, verbose=1,
         params = AnatomicalParams()
         params.num_points = 1
         params.vertebraes = [3, ]
+        params.subtitle = 'Click at the posterior tip of C2-C3 disc'
         input_file = Image(fname)
         output_file = input_file.copy()
         output_file.data *= 0
         output_file.setFileName(os.path.join(path_output, 'labels.nii.gz'))
         controller = launch_sagittal_dialog(input_file, output_file, params)
         mask_points = controller.as_string()
-
-        # assign new init_disc_z value, which corresponds to the first vector of mask_points. Note, we need to substract from nz due to SAL orientation: in the viewer, orientation is S-I while in this code, it is I-S.
-        init_disc = [nz - int(mask_points.split(',')[0]), 2]
+        # assign new init_disc_z value
+        # Note: there is a discrepancy between the label value (3) and the disc value (2). As of mid-2017, the SCT convention for disc C2-C3 is value=3. Before that it was value=2.
+        init_disc = [int(mask_points.split(',')[2]), 2]
 
     # display init disc
     if verbose == 2:

spinalcordtoolbox/gui/base.py

@@ -45,7 +45,8 @@ def __init__(self,
         self.start_vertebrae = 50
         self.end_vertebrae = -1
         self.num_points = 0
-        self._title = ''
+        self._title = ''  # figure title
+        self.subtitle = ''  # subplot title (will be displayed above the image)
         self._vertebraes = []
         self.input_file_name = ""
         self.starting_slice = 0

spinalcordtoolbox/gui/sagittal.py

@@ -55,6 +55,7 @@ def _init_canvas(self, parent):
         vlayout.addWidget(self.axial)
 
         self.sagittal = widgets.SagittalCanvas(self, plot_points=True, annotate=True)
+        self.sagittal.title(self.params.subtitle)
         self.sagittal.point_selected_signal.connect(self.on_select_point)
         layout.addWidget(self.sagittal)