Code cleanup. Instroduced underscore notation for private functions, methods and attributes

cfel_cxi.py

@@ -33,6 +33,7 @@ import numpy
 
 _CXISimpleEntry = namedtuple('SimpleEntry', ['path', 'data', 'overwrite'])
 
+
 class _Stack:
     def __init__(self, path, data, axes):
 
@@ -47,6 +48,13 @@ class _Stack:
         self._path = path
         self._axes = axes
 
+    def is_there_data_to_write(self):
+
+        if self._data_to_write is not None:
+            return True
+        else:
+            return False
+
     def write_initial_slice(self, file_handle, max_num_slices):
 
         file_handle.create_dataset(self._path, shape=(max_num_slices,) + self._data_shape,
@@ -337,7 +345,7 @@ class CXIWriter:
             raise RuntimeError('The file already holds the maximum allowed number of slices, and should be closed')
 
         for entry in self._cxi_stacks.values():
-            if entry._data_to_write is None:
+            if entry.is_there_data_to_write is False:
                 raise RuntimeError('The slice is incomplete and will not be written. The following stack is not '
                                    'present in the current slice:', entry.path)
 
@@ -376,4 +384,4 @@ class CXIWriter:
 
         self._fh.close()
 
-        self._file_is_open = False
\ No newline at end of file
+        self._file_is_open = False

cfel_fabio.py

@@ -64,8 +64,8 @@ def read_cbf_from_stream(stream):
         if len(cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY]) > int(
                 cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(cbf_obj.STARTER):
             cbf_obj.cbs = cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) +
-                                                                         cbf_obj.start_binary +
-                                                                         len(cbf_obj.STARTER)]
+                                                                    cbf_obj.start_binary +
+                                                                    len(cbf_obj.STARTER)]
         else:
             cbf_obj.cbs = cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY]
     binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(cbf_obj.STARTER):]

cfel_vtk.py

@@ -460,8 +460,12 @@ def scatterplot_3d(data, color=None, point_size=None, cmap="jet", point_shape=No
 
         color (Optional[numpy.ndimage]): 1D Array of floating points with same length as the data array.
             These numbers give the color of each point.
+            
         point_size (Optional[float]): The size of each points. Behaves differently depending on the point_shape.
             If shape is spheres the size is relative to the scene and if squares the size is relative to the window.
+            
+        cmap (Optional[str]): Color map
+        
         point_shape (Optional["spheres" or "squares"]): "spheres" plots each point as a sphere, recommended for
             small data sets. "squares" plot each point as a square without any 3D structure, recommended for
             large data sets.