From 5d6cabba5428f9ddf4c4487ffc2668a6fb70cb17 Mon Sep 17 00:00:00 2001 From: Edoardo Pasca Date: Tue, 15 May 2018 16:37:40 +0200 Subject: move padder to plugins (#121) --- Wrappers/Python/ccpi/processors.py | 105 --------------------------------- Wrappers/Python/conda-recipe/meta.yaml | 1 - 2 files changed, 106 deletions(-) (limited to 'Wrappers/Python') diff --git a/Wrappers/Python/ccpi/processors.py b/Wrappers/Python/ccpi/processors.py index b65722e..a2d0446 100755 --- a/Wrappers/Python/ccpi/processors.py +++ b/Wrappers/Python/ccpi/processors.py @@ -19,7 +19,6 @@ from ccpi.framework import DataProcessor, DataContainer, AcquisitionData,\ AcquisitionGeometry, ImageGeometry, ImageData -from ccpi.reconstruction.parallelbeam import alg as pbalg import numpy from scipy import ndimage @@ -389,107 +388,3 @@ class CenterOfRotationFinder(DataProcessor): return cor - -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/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml index c6b1940..f72c980 100644 --- a/Wrappers/Python/conda-recipe/meta.yaml +++ b/Wrappers/Python/conda-recipe/meta.yaml @@ -18,7 +18,6 @@ requirements: run: - python - numpy - #- ccpi-reconstruction - matplotlib about: -- cgit v1.2.3