moves some input checking from the demo scripts into the corresponding methods

Author: joeljonsson

demo/get_apr_interactive_demo.py

@@ -26,9 +26,6 @@ def main():
     fpath = io_int.get_tiff_file_name()  # get image file path from gui (data type must be float32 or uint16)
     img = skio.imread(fpath)
 
-    while img.ndim < 3:
-        img = np.expand_dims(img, axis=0)
-
     # Set some parameters (only Ip_th, grad_th and sigma_th are set interactively)
     par = pyapr.APRParameters()
     par.rel_error = 0.1              # relative error threshold

demo/raycast_demo.py

@@ -21,12 +21,6 @@ def main():
     # Read APR and particles from file
     pyapr.io.read(fpath_apr, apr, parts)
 
-    # Raycast viewer currently only works for ShortParticles
-    if isinstance(parts, pyapr.FloatParticles):
-        tmp = pyapr.ShortParticles()
-        tmp.copy(parts)
-        parts = tmp
-
     # Launch the raycast viewer
     pyapr.viewer.raycast_viewer(apr, parts)
 

pyapr/converter/converter_methods.py

@@ -53,6 +53,9 @@ def get_apr_interactive(image, rel_error=0.1, gradient_smoothing=2, verbose=True
               'input image has been replaced with a C-contiguous copy of itself')
         image = np.ascontiguousarray(image)
 
+    while image.ndim < 3:
+        image = np.expand_dims(image, axis=0)
+
     # Initialize objects
     io_int = pyapr.InteractiveIO()
     apr = pyapr.APR()
@@ -105,6 +108,9 @@ def find_parameters_interactive(image, rel_error=0.1, gradient_smoothing=0, verb
               'input image has been replaced with a C-contiguous copy of itself')
         image = np.ascontiguousarray(image)
 
+    while image.ndim < 3:
+        image = np.expand_dims(image, axis=0)
+
     # Initialize objects
     io_int = pyapr.filegui.InteractiveIO()
     apr = pyapr.APR()

pyapr/viewer/partsViewer.py

@@ -349,26 +349,20 @@ def imageHoverEvent(self, event):
         self.cursor.setText(text_string)
 
 
-def parts_viewer(aAPR, Parts):
-    pg.setConfigOption('background', 'w')
-    pg.setConfigOption('foreground', 'k')
+def parts_viewer(apr, parts):
 
     app = QtGui.QApplication.instance()
     if app is None:
         app = QtGui.QApplication([])
 
+    pg.setConfigOption('background', 'w')
+    pg.setConfigOption('foreground', 'k')
     pg.setConfigOption('imageAxisOrder', 'row-major')
 
-    ## Create window with GraphicsView widget
+    # Create window with GraphicsView widget
     win = MainWindow()
-
     win.add_level_toggle()
-
-    win.init_APR(aAPR, Parts)
-
+    win.init_APR(apr, parts)
     win.show()
 
     app.exec_()
-
-    return None
-

pyapr/viewer/raycastViewer.py

@@ -285,6 +285,15 @@ def valuechangeAniso(self):
 
 def raycast_viewer(apr, parts):
 
+    # Raycast viewer currently only works for ShortParticles
+    if isinstance(parts, pyapr.FloatParticles):
+        print('Warning: raycast_viewer is currently only implemented for ShortParticles. '
+              'Using a uint16 copy of the input particles.')
+        parts_short = pyapr.ShortParticles()
+        parts_short.copy(parts)
+    else:
+        parts_short = parts
+
     pg.setConfigOption('background', 'w')
     pg.setConfigOption('foreground', 'k')
     pg.setConfigOption('imageAxisOrder', 'row-major')
@@ -293,31 +302,23 @@ def raycast_viewer(apr, parts):
     if app is None:
         app = QtGui.QApplication([])
 
-    ## Create window with GraphicsView widget
+    # Create window with GraphicsView widget
     win = MainWindowImage()
-
     win.show()
-
     win.apr_ref = apr
-
     win.app_ref = app
 
     raycaster = pyapr.viewer.raycaster()
-
     raycaster.set_z_anisotropy(1)
     raycaster.set_radius(0.1)
 
     win.view.setMouseEnabled(False, False)
-
     win.raycaster_ref = raycaster
-
     win.raycaster_ref.set_angle(win.current_theta)
     win.raycaster_ref.set_phi(win.current_phi)
 
     tree_parts = pyapr.FloatParticles()
-
     pyapr.viewer.get_down_sample_parts(apr, parts, tree_parts)
 
-    win.set_image(apr, parts, tree_parts)
-
+    win.set_image(apr, parts_short, tree_parts)
     app.exec_()