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-rw-r--r--Wrappers/Python/ccpi/framework.py200
1 files changed, 148 insertions, 52 deletions
diff --git a/Wrappers/Python/ccpi/framework.py b/Wrappers/Python/ccpi/framework.py
index 82ad65c..7324a5c 100644
--- a/Wrappers/Python/ccpi/framework.py
+++ b/Wrappers/Python/ccpi/framework.py
@@ -23,6 +23,7 @@ import numpy
import sys
from datetime import timedelta, datetime
import warnings
+from ccpi.reconstruction import geoms
if sys.version_info[0] >= 3 and sys.version_info[1] >= 4:
ABC = abc.ABC
@@ -119,7 +120,7 @@ class DataSet(object):
if deep_copy:
self.array = array[:]
else:
- self.array = array
+ self.array = array
else:
raise TypeError('Array must be NumpyArray, passed {0}'\
.format(type(array)))
@@ -430,40 +431,81 @@ class DataSet(object):
class VolumeData(DataSet):
'''DataSet for holding 2D or 3D dataset'''
def __init__(self,
- array,
+ array = None,
deep_copy=True,
dimension_labels=None,
**kwargs):
- if type(array) == DataSet:
- # if the array is a DataSet get the info from there
- #if not ( array.number_of_dimensions == 2 or \
- # array.number_of_dimensions == 3 ):
- # raise ValueError('Number of dimensions are not 2 or 3: {0}'\
- # .format(array.number_of_dimensions))
-
- #DataSet.__init__(self, array.as_array(), deep_copy,
- # array.dimension_labels, **kwargs)
- super(VolumeData, self).__init__(array.as_array(), deep_copy,
- array.dimension_labels, **kwargs)
- elif type(array) == numpy.ndarray:
- #if not ( array.ndim == 3 or array.ndim == 2 ):
- # raise ValueError(
- # 'Number of dimensions are not 3 or 2 : {0}'\
- # .format(array.ndim))
+ self.geometry = None
+ if array is None:
+ if 'geometry' in kwargs.keys():
+ geometry = kwargs['geometry']
+ self.geometry = geometry
+ channels = geometry.channels
+ horiz_x = geometry.voxel_num_x
+ horiz_y = geometry.voxel_num_y
+ vert = 1 if geometry.voxel_num_z is None\
+ else geometry.voxel_num_z # this should be 1 for 2D
- if dimension_labels is None:
- if array.ndim == 3:
- dimension_labels = ['horizontal_x' ,
- 'horizontal_y' ,
- 'vertical']
+ if channels > 1:
+ if vert > 1:
+ shape = (channels, vert, horiz_y, horiz_x)
+ dim_labels = ['channel' ,'vertical' , 'horizontal_y' ,
+ 'horizontal_x']
+ else:
+ shape = (channels , horiz_y, horiz_x)
+ dim_labels = ['channel' , 'horizontal_y' ,
+ 'horizontal_x']
else:
- dimension_labels = ['horizontal' ,
- 'vertical']
-
- #DataSet.__init__(self, array, deep_copy, dimension_labels, **kwargs)
- super(VolumeData, self).__init__(array, deep_copy,
- dimension_labels, **kwargs)
+ if vert > 1:
+ shape = (vert, horiz_y, horiz_x)
+ dim_labels = ['vertical' , 'horizontal_y' ,
+ 'horizontal_x']
+ else:
+ shape = (horiz_y, horiz_x)
+ dim_labels = ['horizontal_y' ,
+ 'horizontal_x']
+
+ array = numpy.zeros( shape , dtype=numpy.float32)
+ super(VolumeData, self).__init__(array, deep_copy,
+ dim_labels, **kwargs)
+
+ else:
+ raise ValueError('Please pass either a DataSet, ' +\
+ 'a numpy array or a geometry')
+ else:
+ if type(array) == DataSet:
+ # if the array is a DataSet get the info from there
+ if not ( array.number_of_dimensions == 2 or \
+ array.number_of_dimensions == 3 or \
+ array.number_of_dimensions == 4):
+ raise ValueError('Number of dimensions are not 2 or 3 or 4: {0}'\
+ .format(array.number_of_dimensions))
+
+ #DataSet.__init__(self, array.as_array(), deep_copy,
+ # array.dimension_labels, **kwargs)
+ super(VolumeData, self).__init__(array.as_array(), deep_copy,
+ array.dimension_labels, **kwargs)
+ elif type(array) == numpy.ndarray:
+ if not ( array.ndim == 2 or array.ndim == 3 or array.ndim == 4 ):
+ raise ValueError(
+ 'Number of dimensions are not 2 or 3 or 4 : {0}'\
+ .format(array.ndim))
+
+ if dimension_labels is None:
+ if array.ndim == 4:
+ dimension_labels = ['channel' ,'vertical' , 'horizontal_y' ,
+ 'horizontal_x']
+ elif array.ndim == 3:
+ dimension_labels = ['vertical' , 'horizontal_y' ,
+ 'horizontal_x']
+ else:
+ dimension_labels = ['horizontal_y' ,
+ 'horizontal_x']
+
+ #DataSet.__init__(self, array, deep_copy, dimension_labels, **kwargs)
+ super(VolumeData, self).__init__(array, deep_copy,
+ dimension_labels, **kwargs)
# load metadata from kwargs if present
for key, value in kwargs.items():
@@ -478,34 +520,79 @@ class VolumeData(DataSet):
class SinogramData(DataSet):
'''DataSet for holding 2D or 3D sinogram'''
def __init__(self,
- array,
+ array = None,
deep_copy=True,
dimension_labels=None,
**kwargs):
-
- if type(array) == DataSet:
- # if the array is a DataSet get the info from there
- #if not ( array.number_of_dimensions == 2 or \
- # array.number_of_dimensions == 3 ):
- # raise ValueError('Number of dimensions are not 2 or 3: {0}'\
- # .format(array.number_of_dimensions))
-
- DataSet.__init__(self, array.as_array(), deep_copy,
- array.dimension_labels, **kwargs)
- elif type(array) == numpy.ndarray:
- #if not ( array.ndim == 3 or array.ndim == 2 ):
- # raise ValueError('Number of dimensions are != 3: {0}'\
- # .format(array.ndim))
- if dimension_labels is None:
- if array.ndim == 3:
- dimension_labels = ['angle' ,
- 'horizontal' ,
- 'vertical']
+ self.geometry = None
+ if array is None:
+ if 'geometry' in kwargs.keys():
+ geometry = kwargs['geometry']
+ self.geometry = geometry
+ channels = geometry.channels
+ horiz = geometry.pixel_num_h
+ vert = geometry.pixel_num_v
+ angles = geometry.angles
+ num_of_angles = numpy.shape(angles)[0]
+
+
+ if channels > 1:
+ if vert > 1:
+ shape = (channels, num_of_angles , vert, horiz)
+ dim_labels = ['channel' , ' angle' ,
+ 'vertical' , 'horizontal']
+ else:
+ shape = (channels , num_of_angles, horiz)
+ dim_labels = ['angle' , 'angle' ,
+ 'horizontal']
else:
- dimension_labels = ['angle' ,
- 'horizontal']
- DataSet.__init__(self, array, deep_copy, dimension_labels, **kwargs)
+ if vert > 1:
+ shape = (num_of_angles, vert, horiz)
+ dim_labels = ['angles' , 'vertical' ,
+ 'horizontal']
+ else:
+ shape = (num_of_angles, horiz)
+ dim_labels = ['angles' ,
+ 'horizontal']
+
+ array = numpy.zeros( shape , dtype=numpy.float32)
+ super(SinogramData, self).__init__(array, deep_copy,
+ dim_labels, **kwargs)
+ else:
+ if type(array) == DataSet:
+ # if the array is a DataSet get the info from there
+ if not ( array.number_of_dimensions == 2 or \
+ array.number_of_dimensions == 3 or \
+ array.number_of_dimensions == 4):
+ raise ValueError('Number of dimensions are not 2 or 3 or 4: {0}'\
+ .format(array.number_of_dimensions))
+
+ #DataSet.__init__(self, array.as_array(), deep_copy,
+ # array.dimension_labels, **kwargs)
+ super(SinogramData, self).__init__(array.as_array(), deep_copy,
+ array.dimension_labels, **kwargs)
+ elif type(array) == numpy.ndarray:
+ if not ( array.ndim == 2 or array.ndim == 3 or array.ndim == 4 ):
+ raise ValueError(
+ 'Number of dimensions are not 2 or 3 or 4 : {0}'\
+ .format(array.ndim))
+
+ if dimension_labels is None:
+ if array.ndim == 4:
+ dimension_labels = ['channel' ,'angle' , 'vertical' ,
+ 'horizontal']
+ elif array.ndim == 3:
+ dimension_labels = ['angle' , 'vertical' ,
+ 'horizontal']
+ else:
+ dimension_labels = ['angle' ,
+ 'horizontal']
+
+ #DataSet.__init__(self, array, deep_copy, dimension_labels, **kwargs)
+ super(SinogramData, self).__init__(array, deep_copy,
+ dimension_labels, **kwargs)
+
class DataSetProcessor(object):
'''Defines a generic DataSet processor
@@ -799,4 +886,13 @@ if __name__ == '__main__':
b1 = ds.subset( subset , Z=1)
print ("shape b 2,3? {0}".format(numpy.shape(b1.as_array())))
+
+ # create VolumeData from geometry
+ vgeometry = geoms.VolumeGeometry(voxel_num_x=2, voxel_num_y=3, channels=2)
+ vol = VolumeData(geometry=vgeometry)
+
+ sgeometry = geoms.SinogramGeometry(dimension=2, angles=10,
+ geom_type='parallel', pixel_num_v=3,
+ pixel_num_h=5 , channels=2)
+ sino = SinogramData(geometry=sgeometry)
\ No newline at end of file
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 14:57:26 +0000