unwrap: moved pure python code from unwrap2D.pyx to unwrap.py, allocate output array in pure python

unwrap2D/setup.py

@@ -7,7 +7,6 @@ import numpy as np
 ext_modules = [
     Extension('unwrap2D', 
               ['unwrap2D.pyx',
-               #'Miguel_2D_unwrapper_with_mask_and_wrap_around_option.cpp',
                'Miguel_2D_unwrapper_with_mask_and_wrap_around_option.c',
                ],
               include_dirs = [np.get_include(),],

unwrap2D/test_unwrap.py

@@ -1,5 +1,5 @@
 from numpy.testing import *
-from unwrap2D import unwrap2D
+from unwrap import unwrap2D
 
 import numpy as np
 from numpy import outer, arange, ones, abs, empty, power, indices

unwrap2D/unwrap.py

@@ -0,0 +1,20 @@
+import numpy as np
+from unwrap2D import _unwrap2D
+
+def unwrap2D(wrapped_array, wrap_around_x = False, wrap_around_y = False):
+    wrapped_array = np.require(wrapped_array, np.float32, ['C'])
+    wrapped_array_masked = np.ma.asarray(wrapped_array)
+    unwrapped_array = np.empty_like(wrapped_array_masked.data)
+    
+    _unwrap2D(wrapped_array_masked.data, 
+              np.ma.getmaskarray(wrapped_array_masked).astype(np.uint8),
+              unwrapped_array,
+              wrap_around_x, wrap_around_y)
+    if np.ma.isMaskedArray(wrapped_array):
+        return np.ma.array(unwrapped_array, mask = wrapped_array_masked.mask)
+    else:
+        return unwrapped_array
+
+    #TODO: set_fill to minimum value
+    #TODO: check for empty mask, not a single contiguous pixel
+

unwrap2D/unwrap2D.pyx

@@ -1,41 +1,22 @@
-import numpy as np
-cimport numpy as np
-
-import numpy.ma
-
+#import numpy as np
+#cimport numpy as np
 cdef extern int unwrap(float* wrapped_image, 
                        float* unwrapped_image, 
                        unsigned char* input_mask, 
                        int image_width, int image_height,
                        int wrap_around_x, int wrap_around_y)
 
-def unwrap2D(input, wrap_around_x = False, wrap_around_y = False):
-    
-    masked_array = numpy.ma.asarray(input, dtype = np.float32)
-    unwrapped_array = _unwrap2D(masked_array.data, 
-                                numpy.ma.getmaskarray(masked_array).astype(np.uint8),
-                                wrap_around_x, wrap_around_y)
-    if numpy.ma.isarray(input):
-        return numpy.ma.array(unwrapped_array, mask = input.mask)
-    else:
-        return unwrapped_array
-
-    #TODO: set_fill to minimum value
-    
-
-cdef _unwrap2D(float[:,::1] array, 
+def _unwrap2D(float[:,::1] array, 
                unsigned char[:,::1] mask,
+               float[:,::1] unwrapped_array,
                wrap_around_x, wrap_around_y):
-    cdef float[:,::1] unwrapped_array = np.empty_like(array)
     cdef int h = array.shape[0]
     cdef int w = array.shape[1]
-    #TODO: check for masked array/
     unwrap(&array[0,0], 
            &unwrapped_array[0,0], 
            &mask[0,0], 
            array.shape[0], array.shape[1],
            wrap_around_x, wrap_around_y,
             )
-    return np.asarray(unwrapped_array)