Add tooltips (#104)

brainreg_segment/layout/gui_elements.py

@@ -21,6 +21,7 @@ def add_combobox(
     label_stack=False,
     callback=None,
     width=150,
+    tooltip=None,
 ):
     if label_stack:
         combobox_row = row + 1
@@ -41,6 +42,8 @@ def add_combobox(
     else:
         combobox_label = None
 
+    if tooltip:
+        combobox.setToolTip(tooltip)
     layout.addWidget(combobox, combobox_row, combobox_column)
     return combobox, combobox_label
 
@@ -55,6 +58,7 @@ def add_button(
     visibility=True,
     minimum_width=0,
     alignment="center",
+    tooltip=None,
 ):
     button = QPushButton(label)
     if alignment == "center":
@@ -66,6 +70,9 @@ def add_button(
 
     button.setVisible(visibility)
     button.setMinimumWidth(minimum_width)
+
+    if tooltip:
+        button.setToolTip(tooltip)
     layout.addWidget(button, row, column)
     button.clicked.connect(connected_function)
     return button
@@ -119,33 +126,41 @@ def add_button(
 #     return button
 
 
-def add_checkbox(layout, default, label, row, column=0):
+def add_checkbox(layout, default, label, row, column=0, tooltip=None):
     box = QCheckBox()
     box.setChecked(default)
+    if tooltip:
+        box.setToolTip(tooltip)
     layout.addWidget(QLabel(label), row, column)
     layout.addWidget(box, row, column + 1)
     return box
 
 
 def add_float_box(
-    layout, default, minimum, maximum, label, step, row, column=0
+    layout, default, minimum, maximum, label, step, row, column=0, tooltip=None
 ):
     box = QDoubleSpinBox()
     box.setMinimum(minimum)
     box.setMaximum(maximum)
     box.setValue(default)
     box.setSingleStep(step)
+    if tooltip:
+        box.setToolTip(tooltip)
     layout.addWidget(QLabel(label), row, column)
     layout.addWidget(box, row, column + 1)
     return box
 
 
-def add_int_box(layout, default, minimum, maximum, label, row, column=0):
+def add_int_box(
+    layout, default, minimum, maximum, label, row, column=0, tooltip=None
+):
     box = QSpinBox()
     box.setMinimum(minimum)
     box.setMaximum(maximum)
     # Not always set if not after min & max
     box.setValue(default)
+    if tooltip:
+        box.setToolTip(tooltip)
     layout.addWidget(QLabel(label), row, column)
     layout.addWidget(box, row, column + 1)
     return box

brainreg_segment/segment.py

@@ -154,6 +154,8 @@ def add_segmentation_methods_panel(self, row, column=1):
             column=1,
             minimum_width=COLUMN_WIDTH,
             alignment=SEGM_METHODS_PANEL_ALIGN,
+            tooltip="Segment a 1D structure (e.g. an axon "
+            "or implanted electrode)",
         )
         self.show_trackseg_button.setEnabled(False)
 
@@ -165,6 +167,7 @@ def add_segmentation_methods_panel(self, row, column=1):
             column=1,
             minimum_width=COLUMN_WIDTH,
             alignment=SEGM_METHODS_PANEL_ALIGN,
+            tooltip="Segment a 2/3D structure (e.g. a brain region)",
         )
         self.show_regionseg_button.setEnabled(False)
 
@@ -196,6 +199,10 @@ def add_loading_panel(self, row, column=0):
             visibility=False,
             minimum_width=COLUMN_WIDTH,
             alignment=LOADING_PANEL_ALIGN,
+            tooltip="Load a brainreg project in the coordinate "
+            "space of your raw data (i.e., not warped to the atlas "
+            "space).  N.B. the data will have been reoriented to "
+            "the orientation of your chosen atlas.",
         )
 
         self.load_button_standard = add_button(
@@ -207,6 +214,8 @@ def add_loading_panel(self, row, column=0):
             visibility=False,
             minimum_width=COLUMN_WIDTH,
             alignment=LOADING_PANEL_ALIGN,
+            tooltip="Load a brainreg project warped to the coordinate "
+            "space of the atlas.",
         )
 
         self.add_atlas_menu(self.load_data_layout)
@@ -236,6 +245,9 @@ def add_saving_panel(self, row):
             row=0,
             column=0,
             visibility=False,
+            tooltip="Export the segmentation to brainrender "
+            "(only works if the segmentation was "
+            "performed in atlas space.",
         )
         self.save_button = add_button(
             "Save",
@@ -244,6 +256,7 @@ def add_saving_panel(self, row):
             row=0,
             column=1,
             visibility=False,
+            tooltip="Save the segmentation to disk to " "be reloaded later.",
         )
 
         self.save_data_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
@@ -269,6 +282,9 @@ def add_atlas_menu(self, layout):
                 label_stack=True,
                 callback=self.initialise_atlas,
                 width=COLUMN_WIDTH,
+                tooltip="Load a BrainGlobe atlas if you don't have "
+                "a brainreg project to load. Useful for creating "
+                "illustrations or testing the software.",
             )
 
         self.atlas_menu = atlas_menu

brainreg_segment/segmentation_panels/regions.py

@@ -62,6 +62,8 @@ def add_region_panel(self, row):
             self.add_new_region,
             row=2,
             column=0,
+            tooltip="Create a new empty segmentation layer "
+            "to manually segment a new region.",
         )
 
         add_button(
@@ -70,27 +72,38 @@ def add_region_panel(self, row):
             self.run_region_analysis,
             row=2,
             column=1,
+            tooltip="Analyse the spatial distribution of the "
+            "segmented regions.",
         )
         add_button(
             "Add region from selected layer",
             region_layout,
             self.add_region_from_existing_layer,
             row=3,
             column=0,
+            tooltip="Adds a region from a selected labels layer (e.g. "
+            "from another plugin). Make sure this region "
+            "was segmented from the currently loaded "
+            "brainreg result (i.e. atlas/sample space)!",
         )
 
         self.calculate_volumes_checkbox = add_checkbox(
             region_layout,
             self.calculate_volumes_default,
             "Calculate volumes",
             0,
+            tooltip="Calculate and save the volume of each "
+            "brain region included in the segmented "
+            "region.",
         )
 
         self.summarise_volumes_checkbox = add_checkbox(
             region_layout,
             self.summarise_volumes_default,
             "Summarise volumes",
             1,
+            tooltip="Summarise each segmented region "
+            "(e.g. center, volume etc.).",
         )
 
         region_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)

brainreg_segment/segmentation_panels/tracks.py

@@ -80,6 +80,8 @@ def add_track_panel(self, row):
             self.add_track,
             row=5,
             column=0,
+            tooltip="Create a new empty segmentation layer "
+            "to manually annotate a new track.",
         )
 
         add_button(
@@ -88,6 +90,9 @@ def add_track_panel(self, row):
             self.run_track_analysis,
             row=5,
             column=1,
+            tooltip="Join up the points using a spline fit "
+            "and save the distribution of the track in "
+            "the brain.",
         )
 
         add_button(
@@ -96,6 +101,10 @@ def add_track_panel(self, row):
             self.add_track_from_existing_layer,
             row=6,
             column=0,
+            tooltip="Adds a track from a selected points layer (e.g. "
+            "from another plugin). Make sure this track "
+            "was segmented from the currently loaded "
+            "brainreg result (i.e. atlas/sample space)! ",
         )
 
         add_button(
@@ -104,13 +113,20 @@ def add_track_panel(self, row):
             self.add_surface_points,
             row=6,
             column=1,
+            tooltip="Add an additional first point at the surface of the "
+            "brain. Selecting this option will add an additional "
+            "point at the closest part of the brain surface to the "
+            "first point, so that the track starts there.",
         )
 
         self.summarise_track_checkbox = add_checkbox(
             track_layout,
             self.summarise_track_default,
             "Summarise",
-            0,
+            row=0,
+            tooltip="Save a csv file, showing the brain area for "
+            "each part of the interpolated track "
+            "(determined by the number of spline points). ",
         )
 
         self.fit_degree = add_int_box(
@@ -120,6 +136,7 @@ def add_track_panel(self, row):
             5,
             "Fit degree",
             1,
+            tooltip="Degree of polynomial to fit to the track.",
         )
 
         self.spline_smoothing = add_float_box(
@@ -130,6 +147,9 @@ def add_track_panel(self, row):
             "Spline smoothing",
             0.1,
             2,
+            tooltip="How closely or not to fit the points "
+            "(lower numbers fit more closely, for "
+            "a less smooth interpolation).",
         )
 
         self.spline_points = add_int_box(
@@ -139,6 +159,8 @@ def add_track_panel(self, row):
             10000,
             "Spline points",
             3,
+            tooltip="How many points are sampled from the "
+            "interpolation (used for the summary).",
         )
 
         track_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)