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| author | Edoardo Pasca <edo.paskino@gmail.com> | 2018-05-15 16:37:34 +0200 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2018-05-15 16:37:34 +0200 |
| commit | 4f7b325602e113db8e8ecb4431675b78e4e578dc (patch) | |
| tree | 0eeb88a139a1e156366defc6dd19e58dbc8da829 | |
| parent | ab15b31baf13d3e4528e1cd713ab609a5ed39f0d (diff) | |
| download | framework-plugins-4f7b325602e113db8e8ecb4431675b78e4e578dc.tar.gz framework-plugins-4f7b325602e113db8e8ecb4431675b78e4e578dc.tar.bz2 framework-plugins-4f7b325602e113db8e8ecb4431675b78e4e578dc.tar.xz framework-plugins-4f7b325602e113db8e8ecb4431675b78e4e578dc.zip | |
moved padder to plugins (#14)
| -rwxr-xr-x | Wrappers/Python/ccpi/plugins/processors.py | 103 | ||||
| -rwxr-xr-x | Wrappers/Python/wip/demo_nexus.py | 3 |
2 files changed, 105 insertions, 1 deletions
diff --git a/Wrappers/Python/ccpi/plugins/processors.py b/Wrappers/Python/ccpi/plugins/processors.py index 9938b9e..d31c03b 100755 --- a/Wrappers/Python/ccpi/plugins/processors.py +++ b/Wrappers/Python/ccpi/plugins/processors.py @@ -198,3 +198,106 @@ class CCPiBackwardProjector(DataProcessor): else:
raise ValueError('Cannot process cone beam')
+class AcquisitionDataPadder(DataProcessor):
+ '''Normalization based on flat and dark
+
+ This processor read in a AcquisitionData and normalises it based on
+ the instrument reading with and without incident photons or neutrons.
+
+ Input: AcquisitionData
+ Parameter: 2D projection with flat field (or stack)
+ 2D projection with dark field (or stack)
+ Output: AcquisitionDataSetn
+ '''
+
+ def __init__(self,
+ center_of_rotation = None,
+ acquisition_geometry = None,
+ pad_value = 1e-5):
+ kwargs = {
+ 'acquisition_geometry' : acquisition_geometry,
+ 'center_of_rotation' : center_of_rotation,
+ 'pad_value' : pad_value
+ }
+
+ super(AcquisitionDataPadder, self).__init__(**kwargs)
+
+ def check_input(self, dataset):
+ if self.acquisition_geometry is None:
+ self.acquisition_geometry = dataset.geometry
+ if dataset.number_of_dimensions == 3:
+ return True
+ else:
+ raise ValueError("Expected input dimensions is 2 or 3, got {0}"\
+ .format(dataset.number_of_dimensions))
+
+ def process(self):
+ projections = self.get_input()
+ w = projections.get_dimension_size('horizontal')
+ delta = w - 2 * self.center_of_rotation
+
+ padded_width = int (
+ numpy.ceil(abs(delta)) + w
+ )
+ delta_pix = padded_width - w
+
+ voxel_per_pixel = 1
+ geom = pbalg.pb_setup_geometry_from_acquisition(projections.as_array(),
+ self.acquisition_geometry.angles,
+ self.center_of_rotation,
+ voxel_per_pixel )
+
+ padded_geometry = self.acquisition_geometry.clone()
+
+ padded_geometry.pixel_num_h = geom['n_h']
+ padded_geometry.pixel_num_v = geom['n_v']
+
+ delta_pix_h = padded_geometry.pixel_num_h - self.acquisition_geometry.pixel_num_h
+ delta_pix_v = padded_geometry.pixel_num_v - self.acquisition_geometry.pixel_num_v
+
+ if delta_pix_h == 0:
+ delta_pix_h = delta_pix
+ padded_geometry.pixel_num_h = padded_width
+ #initialize a new AcquisitionData with values close to 0
+ out = AcquisitionData(geometry=padded_geometry)
+ out = out + self.pad_value
+
+
+ #pad in the horizontal-vertical plane -> slice on angles
+ if delta > 0:
+ #pad left of middle
+ command = "out.array["
+ for i in range(out.number_of_dimensions):
+ if out.dimension_labels[i] == 'horizontal':
+ value = '{0}:{1}'.format(delta_pix_h, delta_pix_h+w)
+ command = command + str(value)
+ else:
+ if out.dimension_labels[i] == 'vertical' :
+ value = '{0}:'.format(delta_pix_v)
+ command = command + str(value)
+ else:
+ command = command + ":"
+ if i < out.number_of_dimensions -1:
+ command = command + ','
+ command = command + '] = projections.array'
+ #print (command)
+ else:
+ #pad right of middle
+ command = "out.array["
+ for i in range(out.number_of_dimensions):
+ if out.dimension_labels[i] == 'horizontal':
+ value = '{0}:{1}'.format(0, w)
+ command = command + str(value)
+ else:
+ if out.dimension_labels[i] == 'vertical' :
+ value = '{0}:'.format(delta_pix_v)
+ command = command + str(value)
+ else:
+ command = command + ":"
+ if i < out.number_of_dimensions -1:
+ command = command + ','
+ command = command + '] = projections.array'
+ #print (command)
+ #cleaned = eval(command)
+ exec(command)
+ return out
\ No newline at end of file diff --git a/Wrappers/Python/wip/demo_nexus.py b/Wrappers/Python/wip/demo_nexus.py index 03739b1..ec30fd5 100755 --- a/Wrappers/Python/wip/demo_nexus.py +++ b/Wrappers/Python/wip/demo_nexus.py @@ -12,7 +12,8 @@ from ccpi.framework import ImageData, AcquisitionData, ImageGeometry, Acquisitio from ccpi.optimisation.algs import FISTA, FBPD, CGLS
from ccpi.optimisation.funcs import Norm2sq, Norm1
from ccpi.plugins.ops import CCPiProjectorSimple
-from ccpi.processors import Normalizer, CenterOfRotationFinder, AcquisitionDataPadder
+from ccpi.processors import Normalizer, CenterOfRotationFinder
+from ccpi.plugins.processors import AcquisitionDataPadder
from ccpi.io.reader import NexusReader
# All external imports
|