docstrings, parameter in XYZStackViewer

proxtoolbox/Problems/OrbitalTomog/Graphics/stack_viewer.py

@@ -5,13 +5,19 @@ from matplotlib.widgets import Slider
 
 class SingleStackViewer:
     def __init__(self, volume):
+        """
+        Create window showing a slice of the 3d data, allows to scan the slice position using j, k keys.
+        Note that k will also change the x-axis if the mouse is hovering over the window.
+
+        :param volume: real-valued np.ndarray (3D)
+        """
         fig, ax = plt.subplots()
         ax.volume = volume
         ax.index = volume.shape[0] // 2
         maxval = max(abs(volume))
         im = ax.imshow(volume[ax.index], cmap='seismic', vmin=-maxval, vmax=maxval)
         plt.colorbar(im)
-        ax.set_title('use [j,k] to navigate')
+        ax.set_title('Use [j,k] to navigate')
         fig.canvas.mpl_connect('key_press_event', self.process_key)
 
     def process_key(self, event):
@@ -38,17 +44,20 @@ class SingleStackViewer:
 
 
 class XYZStackViewer:
-    def __init__(self, volume, limit_sliders=(0, 0, 0), cmap='seismic'):
+    def __init__(self, volume, limit_sliders=(0, 0, 0), cmap: str = 'seismic', clim: tuple = (None, None)):
         """
         Dynamic matplotlib plot showing slices out of a 3d dataset
 
         :param volume: real-valued 3d numpy array
         :param limit_sliders: sliders allow range given by [limit, N-limit], where N is the maximal length
         :param cmap: color map to use (e.g. 'seismic' or 'viridis'). For 'seismic, will center on 0, else'
+        :param clim: tuple with the min-max values of the colorscale
         """
         self.volume = volume
 
-        if cmap == 'seismic':
+        if clim[0] is not None:
+            self.minval, self.maxval = clim
+        elif cmap == 'seismic':
             self.maxval = max(abs(volume))
             self.minval = -self.maxval
         else:
@@ -57,7 +66,7 @@ class XYZStackViewer:
         self.indices = [s // 2 for s in volume.shape]
         self.shape = self.volume.shape
 
-        self.fig, self.ax = plt.subplots(1, 3, figsize=(10,4))
+        self.fig, self.ax = plt.subplots(1, 3, figsize=(10, 4))
 
         im = self.ax[0].imshow(volume[self.indices[0], :, :], cmap=cmap, vmin=-self.minval, vmax=self.maxval)
         im = self.ax[1].imshow(volume[:, self.indices[0], :], cmap=cmap, vmin=-self.minval, vmax=self.maxval)
@@ -72,17 +81,17 @@ class XYZStackViewer:
         axcolor = None  # 'lightgoldenrodyellow'
         sliderlength = 0.17
         subax1 = self.fig.add_axes([0.15, 0.1, sliderlength, 0.03], facecolor=axcolor)
-        self.ax1slider = Slider(subax1, 'Slice', 0+limit_sliders[0], self.shape[0]-limit_sliders[0],
+        self.ax1slider = Slider(subax1, 'Slice', 0 + limit_sliders[0], self.shape[0] - limit_sliders[0],
                                 valinit=self.indices[0], valstep=1, valfmt='%d')
         self.ax1slider.on_changed(self.update_1)
 
         subax2 = self.fig.add_axes([0.41, 0.1, sliderlength, 0.03], facecolor=axcolor)
-        self.ax2slider = Slider(subax2, 'Slice', 0+limit_sliders[1], self.shape[0]-limit_sliders[1],
+        self.ax2slider = Slider(subax2, 'Slice', 0 + limit_sliders[1], self.shape[0] - limit_sliders[1],
                                 valinit=self.indices[0], valstep=1, valfmt='%d')
         self.ax2slider.on_changed(self.update_2)
 
         subax3 = self.fig.add_axes([0.67, 0.1, sliderlength, 0.03], facecolor=axcolor)
-        self.ax3slider = Slider(subax3, 'Slice', 0+limit_sliders[2], self.shape[0]-limit_sliders[2],
+        self.ax3slider = Slider(subax3, 'Slice', 0 + limit_sliders[2], self.shape[0] - limit_sliders[2],
                                 valinit=self.indices[0], valstep=1, valfmt='%d')
         self.ax3slider.on_changed(self.update_3)
 
@@ -107,20 +116,3 @@ class XYZStackViewer:
         self.ax[2].images[0].set_array(self.volume[:, :, int(n)])
         self.fig.canvas.draw_idle()
 
-    # def process_key(self, event):
-    #     """Look for special events captured by mpl_connect, send to correct function """
-    #     fig = event.canvas.figure
-    #     ax = fig.axes[0]
-    #     if event.key == 'j':
-    #         self.previous_slice(ax)
-    #     elif event.key == 'k':
-    #         self.next_slice(ax)
-    #     fig.canvas.draw()
-    #
-    # def previous_slice(self, ax):
-    #     """Go to the previous slice on all plots."""
-    #     # do stuff: set_array for all, set self.indices, set_val for sliders
-    #
-    # def next_slice(self, ax):
-    #     """Go to the next slice."""
-    #     # do something