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https://github.com/wassname/scikit-image.git
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unwrap: unified 2d-3d interface, 2d tested ok,
This commit is contained in:
Gregor Thalhammer
committed by
Jostein Bø Fløystad
Jostein Bø Fløystad
parent
1b3b6985f1
commit
96c293ca85
+4
-4
@@ -1015,7 +1015,7 @@ unwrap3D(float* wrapped_volume, float* unwrapped_volume, unsigned char* input_ma
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int volume_width, int volume_height, int volume_depth,
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int wrap_around_x, int wrap_around_y, int wrap_around_z)
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{
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params_t params = {TWOPI, 0, 0, 0, 0}
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params_t params = {TWOPI, wrap_around_x, wrap_around_y, wrap_around_z, 0};
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unsigned char *extended_mask;
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int volume_size = volume_height * volume_width * volume_depth;
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int No_of_Edges_initially = 3 * volume_width * volume_height * volume_depth;
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@@ -1025,8 +1025,8 @@ unwrap3D(float* wrapped_volume, float* unwrapped_volume, unsigned char* input_ma
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EDGE *edge = (EDGE *) calloc(No_of_Edges_initially, sizeof(EDGE));;
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extend_mask(input_mask, extended_mask, volume_width, volume_height, volume_depth, ¶ms);
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initialiseVOXELs(WrappedVolume, input_mask, extended_mask, voxel, volume_width, volume_height, volume_depth);
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calculate_reliability(WrappedVolume, voxel, volume_width, volume_height, volume_depth, ¶ms);
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initialiseVOXELs(wrapped_volume, input_mask, extended_mask, voxel, volume_width, volume_height, volume_depth);
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calculate_reliability(wrapped_volume, voxel, volume_width, volume_height, volume_depth, ¶ms);
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horizontalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, ¶ms);
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verticalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, ¶ms);
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normalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, ¶ms);
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@@ -1041,7 +1041,7 @@ unwrap3D(float* wrapped_volume, float* unwrapped_volume, unsigned char* input_ma
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maskVolume(voxel, input_mask, volume_width, volume_height, volume_depth);
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//copy the volume from VOXELM structure to the unwrapped phase array passed to this function
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returnVolume(voxel, UnwrappedVolume, volume_width, volume_height, volume_depth);
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returnVolume(voxel, unwrapped_volume, volume_width, volume_height, volume_depth);
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free(edge);
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free(voxel);
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@@ -684,7 +684,7 @@ unwrap2D(float* wrapped_image, float* UnwrappedImage, unsigned char* input_mask,
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int image_width, int image_height,
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int wrap_around_x, int wrap_around_y)
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{
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params_t params = {TWOPI, 0, 0, 0};
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params_t params = {TWOPI, wrap_around_x, wrap_around_y, 0};
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unsigned char *extended_mask;
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int image_size = image_height * image_width;
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int No_of_Edges_initially = 2 * image_width * image_height;
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+57
-16
@@ -1,30 +1,51 @@
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from numpy.testing import *
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from unwrap import unwrap2D
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from unwrap import unwrap
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import numpy as np
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from numpy import outer, arange, ones, abs, empty, power, indices
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import numpy.ma as ma
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def test_unwrap2D():
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nx, ny = 32, 32
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nx, ny = 16, 32
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x = np.arange(nx)
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y = np.arange(ny)
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x.shape = (1,-1)
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y.shape = (-1,1)
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x.shape = (-1,1)
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y.shape = (1,-1)
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z = np.exp(1j*x*0.2*np.pi) * np.exp(1j*y*0.1*np.pi)
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phi_w = np.angle(z)
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phi = unwrap2D(phi_w)
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phi = unwrap(phi_w,
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wrap_around_axis_0 = False)
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mask = 0*np.ones((nx, ny), dtype = np.uint8)
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mask[4:16, 4:16] = 1
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phi_w_ma = ma.array(phi_w, dtype = np.float32, mask = mask)
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phi_ma = unwrap2D(phi_w_ma)
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phi_w_ma = np.ma.array(phi_w, dtype = np.float32, mask = mask)
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phi_ma = unwrap(phi_w_ma)
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return (phi_w/(np.pi*2), phi/(np.pi*2),
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return (phi/(np.pi*2),
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phi_w/(np.pi*2), phi/(np.pi*2),
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phi_w_ma/(np.pi*2), phi_ma/(np.pi*2),)
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def test_unwrap3D():
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x, y, z = np.ogrid[:8, :8, :4]
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phi = 2*np.pi*(x*0.2 + y*0.1 + z*0.05)
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phi_wrapped = np.angle(np.exp(1j*phi))
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phi_unwrapped = unwrap(phi_wrapped)
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mask = np.zeros_like(phi, dtype = np.uint8)
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mask[4:6, 4:6, 1:3] = 1
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phi_wrapped_masked = np.ma.array(phi_wrapped, dtype = np.float32, mask = mask)
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phi_unwrapped_masked = unwrap(phi_wrapped_masked)
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s = np.round(phi_unwrapped[0,0,0]/(2*np.pi))
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assert_array_almost_equal(phi/(2*np.pi), phi_unwrapped/(2*np.pi) - s, decimal = 5)
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assert_array_almost_equal(phi + 2*np.pi*s, phi_unwrapped_masked, decimal = 5)
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return (phi/(np.pi*2),
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phi_wrapped/(np.pi*2), phi_unwrapped/(np.pi*2),
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phi_wrapped_masked/(np.pi*2), phi_unwrapped_masked/(np.pi*2),)
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# class test_unwrap(TestCase):
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# def test_simple2d(self, level=1):
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@@ -52,15 +73,35 @@ def test_unwrap2D():
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if __name__=="__main__":
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#NumpyTest().run()
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import matplotlib.pyplot as plt
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p1,p2,p3,p4 = test_unwrap2D()
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p0,p1,p2,p3,p4 = test_unwrap2D()
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plt.figure(1)
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plt.clf()
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plt.subplot(221)
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plt.subplot(322)
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plt.imshow(p0,interpolation = 'nearest')
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plt.subplot(323)
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plt.imshow(p1,interpolation = 'nearest')
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plt.subplot(222)
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plt.subplot(324)
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plt.imshow(p2, interpolation = 'nearest')
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plt.subplot(223)
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plt.subplot(325)
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plt.imshow(p3, interpolation = 'nearest')
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plt.subplot(224)
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plt.subplot(326)
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plt.imshow(p4, interpolation = 'nearest')
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plt.draw()
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p0,p1,p2,p3,p4 = test_unwrap3D()
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plt.figure(2)
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plt.clf()
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plt.subplot(322)
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plt.imshow(p0[:,:,0],interpolation = 'nearest')
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plt.subplot(323)
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plt.imshow(p1[:,:,0],interpolation = 'nearest')
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plt.subplot(324)
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plt.imshow(p2[:,:,0], interpolation = 'nearest')
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plt.subplot(325)
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plt.imshow(p3[:,:,0], interpolation = 'nearest')
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plt.subplot(326)
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plt.imshow(p4[:,:,0], interpolation = 'nearest')
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plt.draw()
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plt.show()
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+21
-7
@@ -1,15 +1,29 @@
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import numpy as np
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from unwrap2D import _unwrap2D
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def unwrap2D(wrapped_array, wrap_around_x = False, wrap_around_y = False):
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def unwrap(wrapped_array,
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wrap_around_axis_0 = False,
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wrap_around_axis_1 = False,
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wrap_around_axis_2 = False):
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wrapped_array = np.require(wrapped_array, np.float32, ['C'])
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if wrapped_array.ndim not in [2,3]:
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raise ValueError('input array needs to have 2 or 3 dimensions')
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wrapped_array_masked = np.ma.asarray(wrapped_array)
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unwrapped_array = np.empty_like(wrapped_array_masked.data)
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_unwrap2D(wrapped_array_masked.data,
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np.ma.getmaskarray(wrapped_array_masked).astype(np.uint8),
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unwrapped_array,
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wrap_around_x, wrap_around_y)
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if wrapped_array.ndim == 2:
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import unwrap2D
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unwrap2D._unwrap2D(wrapped_array_masked.data,
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np.ma.getmaskarray(wrapped_array_masked).astype(np.uint8),
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unwrapped_array,
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bool(wrap_around_axis_0), bool(wrap_around_axis_1))
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elif wrapped_array.ndim == 3:
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import unwrap3D
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unwrap3D._unwrap3D(wrapped_array_masked.data,
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np.ma.getmaskarray(wrapped_array_masked).astype(np.uint8),
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unwrapped_array,
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bool(wrap_around_axis_0), bool(wrap_around_axis_1), bool(wrap_around_axis_2))
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if np.ma.isMaskedArray(wrapped_array):
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return np.ma.array(unwrapped_array, mask = wrapped_array_masked.mask)
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else:
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@@ -13,7 +13,7 @@ def _unwrap2D(float[:,::1] array,
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unwrap2D(&array[0,0],
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&unwrapped_array[0,0],
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&mask[0,0],
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array.shape[0], array.shape[1],
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array.shape[1], array.shape[0],
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wrap_around_x, wrap_around_y,
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)
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@@ -11,7 +11,7 @@ def _unwrap3D(float[:,:,::1] array,
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unwrap3D(&array[0,0,0],
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&unwrapped_array[0,0,0],
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&mask[0,0,0],
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array.shape[0], array.shape[1], array.shape[2],
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array.shape[0], array.shape[1], array.shape[2], #TODO: check!!!
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wrap_around_x, wrap_around_y, wrap_around_z,
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)
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