Commit 0ea23c28d333b28d587bf2a553de953f69e690c6
1 parent
0c04cf8c
Exists in
master
Moved pad_image to surface_process
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2 changed files
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21 additions
and
22 deletions
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invesalius/data/imagedata_utils.py
| @@ -751,22 +751,3 @@ def imgnormalize(data, srange=(0, 255)): | @@ -751,22 +751,3 @@ def imgnormalize(data, srange=(0, 255)): | ||
| 751 | datan = datan.astype(numpy.int16) | 751 | datan = datan.astype(numpy.int16) |
| 752 | 752 | ||
| 753 | return datan | 753 | return datan |
| 754 | - | ||
| 755 | - | ||
| 756 | -def pad_image(image, pad_value, pad_bottom, pad_top): | ||
| 757 | - dz, dy, dx = image.shape | ||
| 758 | - z_iadd = 0 | ||
| 759 | - z_eadd = 0 | ||
| 760 | - if pad_bottom: | ||
| 761 | - z_iadd = 1 | ||
| 762 | - dz += 1 | ||
| 763 | - if pad_top: | ||
| 764 | - z_eadd = 1 | ||
| 765 | - dz += 1 | ||
| 766 | - new_shape = dz, dy + 2, dx + 2 | ||
| 767 | - | ||
| 768 | - paded_image = numpy.empty(shape=new_shape, dtype=image.dtype) | ||
| 769 | - paded_image[:] = pad_value | ||
| 770 | - paded_image[z_iadd: z_iadd + image.shape[0], 1:-1, 1:-1] = image | ||
| 771 | - | ||
| 772 | - return paded_image |
invesalius/data/surface_process.py
| @@ -14,7 +14,6 @@ import vtk | @@ -14,7 +14,6 @@ import vtk | ||
| 14 | import invesalius.i18n as i18n | 14 | import invesalius.i18n as i18n |
| 15 | import invesalius.data.converters as converters | 15 | import invesalius.data.converters as converters |
| 16 | from invesalius.data import cy_mesh | 16 | from invesalius.data import cy_mesh |
| 17 | -import invesalius.data.imagedata_utils as iu | ||
| 18 | 17 | ||
| 19 | import weakref | 18 | import weakref |
| 20 | from scipy import ndimage | 19 | from scipy import ndimage |
| @@ -41,6 +40,25 @@ def ResampleImage3D(imagedata, value): | @@ -41,6 +40,25 @@ def ResampleImage3D(imagedata, value): | ||
| 41 | return resample.GetOutput() | 40 | return resample.GetOutput() |
| 42 | 41 | ||
| 43 | 42 | ||
| 43 | +def pad_image(image, pad_value, pad_bottom, pad_top): | ||
| 44 | + dz, dy, dx = image.shape | ||
| 45 | + z_iadd = 0 | ||
| 46 | + z_eadd = 0 | ||
| 47 | + if pad_bottom: | ||
| 48 | + z_iadd = 1 | ||
| 49 | + dz += 1 | ||
| 50 | + if pad_top: | ||
| 51 | + z_eadd = 1 | ||
| 52 | + dz += 1 | ||
| 53 | + new_shape = dz, dy + 2, dx + 2 | ||
| 54 | + | ||
| 55 | + paded_image = numpy.empty(shape=new_shape, dtype=image.dtype) | ||
| 56 | + paded_image[:] = pad_value | ||
| 57 | + paded_image[z_iadd: z_iadd + image.shape[0], 1:-1, 1:-1] = image | ||
| 58 | + | ||
| 59 | + return paded_image | ||
| 60 | + | ||
| 61 | + | ||
| 44 | def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, | 62 | def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, |
| 45 | mask_dtype, roi, spacing, mode, min_value, max_value, | 63 | mask_dtype, roi, spacing, mode, min_value, max_value, |
| 46 | decimate_reduction, smooth_relaxation_factor, | 64 | decimate_reduction, smooth_relaxation_factor, |
| @@ -60,7 +78,7 @@ def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, | @@ -60,7 +78,7 @@ def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, | ||
| 60 | dtype=mask_dtype, | 78 | dtype=mask_dtype, |
| 61 | shape=mask_shape) | 79 | shape=mask_shape) |
| 62 | if fill_border_holes: | 80 | if fill_border_holes: |
| 63 | - a_mask = iu.pad_image(mask[roi.start + 1: roi.stop + 1, 1:, 1:], 0, pad_bottom, pad_top) | 81 | + a_mask = pad_image(mask[roi.start + 1: roi.stop + 1, 1:, 1:], 0, pad_bottom, pad_top) |
| 64 | else: | 82 | else: |
| 65 | a_mask = numpy.array(mask[roi.start + 1: roi.stop + 1, 1:, 1:]) | 83 | a_mask = numpy.array(mask[roi.start + 1: roi.stop + 1, 1:, 1:]) |
| 66 | image = converters.to_vtk(a_mask, spacing, roi.start, "AXIAL", padding=padding) | 84 | image = converters.to_vtk(a_mask, spacing, roi.start, "AXIAL", padding=padding) |
| @@ -72,7 +90,7 @@ def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, | @@ -72,7 +90,7 @@ def create_surface_piece(filename, shape, dtype, mask_filename, mask_shape, | ||
| 72 | dtype=mask_dtype, | 90 | dtype=mask_dtype, |
| 73 | shape=mask_shape) | 91 | shape=mask_shape) |
| 74 | if fill_border_holes: | 92 | if fill_border_holes: |
| 75 | - a_image = iu.pad_image(image[roi], numpy.iinfo(image.dtype).min, pad_bottom, pad_top) | 93 | + a_image = pad_image(image[roi], numpy.iinfo(image.dtype).min, pad_bottom, pad_top) |
| 76 | else: | 94 | else: |
| 77 | a_image = numpy.array(image[roi]) | 95 | a_image = numpy.array(image[roi]) |
| 78 | # if z_iadd: | 96 | # if z_iadd: |